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If you paint matte, best practice is to apply gloss first anyway.
Matte clear isn't as strong as gloss... it has a chemical accelerant in it which forces it to cure faster, preventing it from forming that glassy skin you get with gloss.Get the gloss on there, allow it to part cure for a few days, then wet-flat it at 500-800 grit (depending on your confidence) and then get the matte over the top. the matte will land flatter and look cleaner overall.
In my humble opinion, matt is almost never worth it if you actually intend to use your bike.
Matte can't be de-nibbed very well whilst refinishing so you can end up with greater surface inclusion and it can't be polished if you scratch it. If you get thigh rub or you have any kind of luggage rubbing on a matte finish, it will actually buff it up.A good budget way to get a non-gloss finish without re-clearing is to throw a few quid at something like Rupes wetflatting discs or 3m Trizact at 3000-6000 grit and use that very wet, with a soft interface pad all-over the bike. It will dull off the sheen enough to give you the matte effect without having to re-clear it.
In terms of pairing different types of products together, try wherever you can to use products designed to work together. The solvents will interact in order to give an optimal chemical bond. There are many exceptions to these rules but if you don't know them, play safe.
Having the finish LOOK good is only one part of it... what's the point in having a five-colour airbrushed graphic under matte clear if you're going to scratch it in a day?
I've got a 2K glossy clear coat. If I was to put it on and decide that I want it matte. Would it be a problem to put matte clear coat on top of it?
In that case would it have to be 2K as well or would an acetone based paint work?