Be aware that you don't simply switch out the mushroom lights for recessed lights. A single mushroom light will provide much more light than a single recessed light. Recessed lighting is very inefficient. A single mushroom light might light up a whole room, whereas you may need 8 recessed lights to accomplish the same thing.
So the charge per recessed light is not just for the recessed light. It's for the wiring, and the extra work that is required to drywall the ceiling.
And it's easier to do now than later.

I guess I should provide more detail. The lights in question are not for any specific rooms, they are hall lights mostly around the home. My concern is there more of a cost/effort to do them latter than a quoted price of 100 per light.

I hope that makes sense.

If it is purely switching out the mushrooms for recessed lights, then that's probably a fairly simple thing to do later.
But as I said before, I doubt that that is all you'd do. A single recessed light won't be much use. You'll most likely be adding additional lights.
So you'd have to fish wires behind finished walls/ceilings. That might mean cutting holes in your nice new drywall. If there's a texture on that drywall, that adds to the complication.
As I said, it's much easier to do before the drywall goes up. The price you were quoted is pretty standard. You MIGHT be able to do it cheaper afterwards, but then again, you might spend a lot more. There are a lot of factors that can affect the price.

Even if you don't have to install additional lights $100 seems to be a fair price. The can is going to run about $16 (at a discount) and the trim can run you somewhere between $5 on up. The box for the light will have to come out and you hope that they didn't short you on the wire lengths for your remodel can (or you're going to have to do more work) and if we're talking about a room with insulation above, it could be messy and annoying in the best of situations.

it's going to cost you more if you do it later.
They'll need to remove the light, cut out the box that the old light was mounted to (which can be a major pain if there's something in the way, plumbing, gas pipe, etc... I've been down this road many times), cut the sheetrock so that they can install a remodel can (which will be way more than $16... and again may not even be possible if the required depth isn't there), wire, trim, lamp, etc...

it's better to do it on new construction if possible. Yes it can be done, but I guarantee you'll be paying more than $100 a can if you do it later.

Thanks for the info. This is just what I needed to make a decision.

@ 100.00 per can-DO IT NOW-
That cost difference in the mortgage will be about $1.00/month, if that!

I get around $125 per recessed light new work.

You have to remember, it's not just the actual can itself you are paying for.