Not only can the mods be removed, I would even say they are quite "tasteful" . I think the mods you listed are actually almost a must have/done thing. If you sell the car on, the new owner is going to be more than likely glad they were done.
Whenever I've modded a car I've owned, I always tried and go for things that were basically offered by the manufacturer as an optional extra/ was used in a different domestic market (for example, with my Impreza P1, I changed the UK spec rear light clusters for the JDM spec, as they looked much cleaner). The other rule I used, was making sure anything I was putting on, was period correct. In my E30 Alpina, it's was a Lachs Silver car and had a grey cloth interior and I managed to put together a full Hounds-tooth cloth one, which was a rare, but was around in the mid 80's when Sytner build my Alpina.
Like the OP, I have managed to get myself a very nice clean example of an E85 M (with a lot more miles sadly) and while I really love the car thus far, there are things I want to change. The original owner, did'nt add on too many options when it was being specced out. I really don't like the carbon black on black leather. I would rather have some contrasts in colour/shade, which will be solved by getting it wrapped, as it can be reversed.
The carbon CSL airbox , like the CSL wheels, is pretty much a universally loved mod to do with our cars, so I would claim that there is no risk of devaluing from doing this by itself. I almost choked on my drink when I saw how much they cost! But when mixed with a more free flowing exhaust, it does make the car sound like a touring car from the 00's. I mean how epic it would be to have all that music happening and you can put the roof down and get the full volume of everything!