I've been hoarding at least one piece of each unique clothing I find in game and decided to pull it all out to mess around. I could not find any outfits that I can wear under the various armor pieces other than vault suits. Similarly no other types of outfits can be upgraded on an armor workbench.

I get that some outfits are too big to work due to clipping issues, but the majority seem like they would work just fine. Am I missing something here?

Also, if this is the case, what benefit would there be to wearing clothing that offers SPECIAL bonuses other than Charisma for trading (the exception being headgear since there is less armor sacrifice)?

road leather

There are tons.

Military fatigues
Gunners flannel and jeans
Raider leathers
Long johns

List goes on

I believe the brotherhood cloths can be worn with additional armor pieces.

Raider and Road Leather armor can be worn with armor pieces - Outside of that, I do not know of any others

The military fatigues do, and the raider leathers, long johns, harness etc.

BOS Uniform.

what outfits can go with armor seems a little bit arbitrary but there is a decent amount of things that work with it

Minuteman outfit

Longjohns?

"underwear" are any pieces that do not make the vault boy flash animate when you are looking at them on your pip boy. These go under your armor. If you are looking at an outfit, and the pieces of armor flash on the vault boy, then this will override the armor and equip, but if it doesn't flash, this is underwear or "underarmor"

Are there any other that can be upgraded? Haven't come across one in ~60 hours.

Nope vault suit is the only one, which is why it's the single best piece of underarmor you can have.

But it looks silly

Well, mods it is

It's actually not such a long list.... It's a bummer

Looks better when you get higher level armor, way way better.

There are others like the Military Fatigues, but they can only be upgraded after doing a certain Railroad quest. You don't have to side with them, just do the quest. Unfortunately I can't remember which one or how to start it.

There's a mod on the Nexus that lets armor be worn with everything. Dresses, suits etc.. Should have downloaded it when I saw it as I can't seem to find it now.

Found it http://www.nexusmods.com/fallout4/mods/745/?

Read the posts for possible problems with the pipboy.

Oh good, i still have avoided all factions quests.

The last element of the list: "List goes on"

There is no concrete list at the moment so everyone just mentions from their memory.

List of under-armor from the official guide:

- Army Fatigues

- Baseball Uniform

BoS Officer Uniform

BoS Uniform

Brotherhood of Steel Uniform (not sure if this is a typo; guide literally lists BoS uniform and Brotherhood of Steel Uniform)

Corset

- Dirty Army Fatigues

Flannel Shirt and Jeans

- Green Shirt and Combat Boots

Gunner Flannel Shirt and Jeans

Gunner Harness

Gunner Leathers

Harness

Long Johns

- Military Fatigues

- Minuteman Outfit

Raider Leathers

Road Leathers

Synth Uniform (2 types)

- Tattered Rags

Undershirt and Jeans

- All Vault Suits

That's the entire list of under-armors. Anything marked with a - can be upgraded; however, in order to upgrade anything that isn't a Vault Suit, you need to find the Railroad. Once you do, you're given a quest called 'Tradecraft'. Complete this, and you'll have access to the Railroad HQ, where you will find P.A.M. Talk to her to get the quest 'Jackpot'. Once complete, talk to Tinker Tom, and you'll be able to modify the indicated under-armors.

I have been wearing the Minuteman Outfit exclusively in the armor.

A lot of those are unobtainable like the synth uniform, only synths wear them and you can't loot it from them.

tshirt and jeans

Just retyping the list from the guide. Haven't verified most of it.