Clothes could probably be synthetically made, although you may have a point there in terms of what would be cheaper. Not all clothing is animal based though (cotton, flax, polyester, etc.).
With regards to the matter conversion, yes that is helpful, but that assumes that a colony would be growing crops that need conversion to a useful form. One would think that a martian greenhouse would only contain crops fairly useful to the colony.
Synthetically made out of what?
Keep in mind that we are not talking about an isolated outpost with regular supply runs to the home culture or a mission of finite length.
We are talking about transplanting civilization.
Just because a plant is useful to the colony doesn't mean that 100% of it's mass is useful. What do you do with the rest of a the cotton plant after you've converted it's seed pod to textiles? The stalks and leaves are toxic to humans but goats or sheep will convert that waste mass into wool, milk, meat, and fertilizer.
NASA actually did a bunch of studies on this back in the 70s on self-sufficient colonies and generation ships. I'll link once I'm back on my home computer. One of the more interesting conclusions was that over a long enough mission timeline (one measured in decades rather than years) certain types of livestock actually constituted a significant mass savings as they negated the need for certain types of consumables and and occupied less volume than an equivalent stockpile of stores.
The break even point was just over a year in most cases. Any longer than that and it became cheaper in terms of mass, energy, and volume to pack chickens and chicken feed than it was to pack an equivelant amount of eggs.
I think the real point here is that the amount of livestock off-planet will be much lower per capita than on earth. Theres just not enough room, consumables, or reason to do it on a large scale.
All this had made me think though, it would be interesting to do a sort of Orbiter Greenhouse project, modelling what gets grown, & what it produces. Maybe Ill try that someday.
Perhapse, the types of livestock will certainly be different. More Caprinae few if any Bovinae. Also expect to see a lot of fish as well. Algae tanks are tend to be more efficient O2 processors than free-standing plants and there's no reason not to have the tanks serve dual purpose as an aquarium / seafood buffet.