Well, first off, I'm glad you got it sorted out on your own.
Now let me just answer your questions for reference or whatever.
Wait ???? are you saying your mod access the RT folder from Roberts Male Body? So then I double checked my robert's install and as I have it the RT folder is not accessed by the Roberts mod at all (it is just a repository for optional meshes for nvde, clothed, and type of clothed) - hence my bain package for Roberts doe not maintain an RT folder on my hard drive because all those options are now BAIN subpackages. So If I chose nvde options for Roberts male then then used the clothed option for SAF that may have caused the missing crotch - it just looks like flesh with missing parts is all.
As written in the post above the underwear on the clothed lowerbodies is matching the options in Robert's V4 body replacer. I even kept the numbers Robert gave the several options, for recognizeability(is that even a word?).
Now those files technically "include" the exact same underwear meshes from Robert's V4 (maybe I had to fix some clipping now and then), thus they will of course need the "underwear textures" from Robert's V4.
In a valid Robert's V4 install these will be found inside "textures/clothes/rt". In Robert's V3 they apparently were somewhere else, thus some people got "missing textures" (in most cases "missing normalmaps" somehow overruled and made the underwear "invisible"). So I thought that would be the case for you, too.
Now if your BAIN package left out those underwear textures because you chose the nvde meshes, then this explains it. Mystery solved.
You just using the nvde alternative from SAF was the ideal solution in your case. Everything's fine.
Otherwise I'm not sure what alternatives folder you mention - I didn't see one in the SAF folders.
Do you mean the folder containing the malelegs_ABfeet.nif type files?
Repeating my last post:
Hmm, I just realized the currently downloadable SAF readme is missing vital contents I very well have written down already in a not-yet-released new SAF readme on my drive.
Now that's a fine place, on my drive... where oh so many downloaders can of course read it at every time! *sarcasm off*
Well, here's the line that "should" be in there. You will notice it was written with a future update in mind, because there is no "alternatives" folder yet. But the files it's talking about are all to be found inside the "argonian" folder, so it's still valid.
QUOTE---
By default these will be underwear option 2 (the vanilla loincloth) for Robert's and Worksafe-Linen Underwear for TFF.
If you opt to use nvde lowerbodies (mammalian or reptilian) or just another underwear option from Robert's, you'll find those inside the "alternatives" folder.
Simply copy the ones you prefer into "\meshes\characters\argonian" and rename them to replace the defaults (make backups in case you reconsider later).
Their names should be self-explaining, the numeration of underwear alternatives matches the numeration Robert uses.
---
So yeah, here we're back at the dreaded "renaming" business (even dreaded by myself now for obvious reasons).
Maybe you could create another alternative sub-package for each of the alternative "malelegs..." (or "femalelegs..." for that matter) found inside there. But is it even a valid step to do this for single files?
The file "malelegs_ABfeet.nif" is the only one the ESP will use. The others were just added on request for a little variety, public convenience and to be able to make the undergarments (if any) of your Argonians matching to your other races'. "malelegs" is the name, "_ABfeet" the tag for my scripts to recognize it as "adapted", and any rest is just telling which alternative it is.
I'll try renaming the nvde versions to see if that works (don't recall that from the readme).
also it might help reducing the confusion in stating what all those alternatives are - such as the mammalian one???
I did post before asking if the SAF meshes folder was good to go as is.
As written the explanation should have been inside the readme already but never got there.
Although... I always thought it would be rather ovious what a "mammal" is in contrast to a "reptile"... especially regarding their genitals.
Alright, guess I will just rename "mammalian" into "human" next and it hopefully will get more clear.
(I must be nuts for wanting my reptiles to have reptilian anatomy below, why I even started creating this "neuter" lowerbody alternative... oh, my)

(in case it's unclear, no offense given or taken, just ridiculing myself here)
Oh, I hope the purpose of those meshes is no longer "arcane and mysterious" to you now. ^_^
Yes, BAIN seems to be quite a worthy alternative to OMODs. And as you can of course even create an installation script using the BAIN folders (folders are folders, eh?), they're also good to go "together".
Variety... I love it!
As for your question in the RBP thread and why following this guide you linked did not work...
well, first of all, it's mentioned in the RBP readme as far as I remember that even the few cosmetic options nowadays in it are actually just "left-overs" from a time when there was no merging with Wrye Bash. So I can perfectly understand it, if bg never even considers adding in more of these.
However, you doing it yourself did not work because you missed out on the secret that is called "mod isolation". You cannot just use an ESP as a master for another ESP with the CS. It's a bit more tricky.
By putting the hairstyles from this one mod into the Argonian racial definition you made RBP require this other plugin as a master. This "will" work when this other plugin gets "ESMified" via Wrye Bash first.
Actually the difference between an ESM and an ESP is just a little flag in the header telling "Hey, I am an ESM!" or not. So ESMifying is as simple as a single click in Wrye Bash's context menu.
Once it is an ESM you can open RBP, which now has it as master, and will have all those hairstyles. However, if you turn it back into an ESP (likewise just a click in bash), and you open RBP ever again, the hairstyles will again be missing. Keep also in mind that not all ESPs can really be used as ESMs "in the game". Some contents might conflict with other ESMs and there is no real rule to which one will win then.
I'm using this quick "ESMify masters" - "open my plugin in the CS, do the changes, save and close" - "ESPify masters again" workflow for a few things myself already. It's really easy once you got a hang of it.
Alternatively you could of course just move over the hair records themselves from the one ESP to the RBP ESP first, save, close, open without the other ESP as master (all hairstyles should be part of RBP now anyways) and then put them into the lists for the Argonian race. But that might of course get quite complex easily, considering the number of different hairstyles there are.