I tend to think of FM: Mercs as a better resource for this topic. As it actually devoted a section to aerospace support in the mercenary industry.
It doesn't say it's just the purview of large units and Great Houses. What it says is that mercs tend to rely on fewer ASFs because they view them as a poor investment. A damaged or destroyed 'mech or tank might be salvaged to some degree. But a destroyed ASF is likely to be a total writeoff because it came apart in the crash or went off into the void of space. So, they tend to rely on fewer ASFs and put veteran pilots in them who are more likely to bring the craft back safely.
It says that mercenaries tend to rely on a formula of 1:12, meaning 1 ASF for every 12 BattleMechs. Whereas the Great Houses double that as standard doctrine.
In practice, fighters still work in pairs, so the smallest unit of fighters that is standard is an aerolance of 2. It just means that while the average Great House might think of standard ASF support for a BattleMech regiment as being approximately 18 fighters. A mercenary BattleMech regiment might run with fewer, more like a squadron or two.
In practice we see plenty of mercenary units of all sizes operate with ASFs, and plenty have full squadrons and wings of them. But a few do notably seem to lack them, probably counting on employer provided air support getting tacked on as part of the contract. So the reality I'm sure varies a lot from unit to unit.
As for swapping out bays. We know it happens sometimes. We have writeups of some merc units here and there that say things like "the dropship <insert name> has been modified to carry the entire unit comfortably."
So it can happen, does happen.
But I'd be just as likely to leave the bays intact. Still need air support, that's still a thing. If the employer is willing to attach some House fighters to my merc unit, I might offer to carry them in my dropship. The employer might find that more agreeable in contract negotiations than having to supply not only some fighters, but also a Leopard-CV or some other carrier dropship for them.
We also have in BT history, plenty of references of smaller specialized merc commands. Think an independent merc fighter squadron here and there. The kind of units you might sub-contract, to tack on to your command to fill the fighter support gap on a more temporary basis. Some of those might have their own dropship support or they might not, and just like employer-provided fighters, need bays to operate out of.
When those bays aren't actively being used for fighters, I don't think it's hard to dream up other uses for them. I forget what canon rules actually say on this. But I used to be in a game where we had an in-house gaming group rule that said it was acceptable to put VTOLs in ASF bays, and they could launch/recover from them when the dropship was landed, and so that was a common alternative use for those bays.
EDIT: Personally, I'd rather have a few ASFs. Seen plenty of "C" grade canon merc units who have at least an aerolance with them. I'd probably go that route to have some air power rather than risk having nothing at all. We've even seen this with cash-strapped mercs, like Avanti's Angels. The novel depicting the Angels in Canopian employ found themselves working with a couple Canopian pilots (government pilots, not mercs), one of them they eventually recruited into the unit, they picked up a couple "old but serviceable Stingrays" to create an aero lance and have some basic fighter support that they added to their roughly battalion-size unit (2 'mech companies and one company of mixed infantry and vehicles). That kind of thing seems pretty normal in the merc world and actually fits nicely with the aforementioned 1:12 formula.
