I have a FCOM modded game which is up and running with my character at level 2.

Now I'm having second thoughts about adding a few DLCs, but I believe it is better to install them before any other mods, as I have done in the past.

So my question is - since they are in .exe form and so cannot take advantage of the safer BAIN install method, is it safe to install them now, or will they overwite crucial parts and so screw up my FCOM game?

It's not that the DLCs have to be installed before any mods, they have to load before any mods. And, within themselves, they have a certain load order. However, BOSS will take care of that for you, so, just install the DLCs, then run BOSS, then make your Merged Patches and you should be good to go.