2001 GS500 with 2004 carbs. Found one #17.5 pilot jet and one #20 pilot jet.

Ordered replacement jets, size #20, only difference
tip diameter is 2.0 mm, originals were 2.5 mmm.

Will the difference disturb the idle, or improve it?

Diffwrence is compensated with idle mixture screw, if it is tapped unblock it. 20 clogs less

Started right up, choke idle a little high, so backed down to around 3,000 rpm;
seemed to warm up pretty fast, maybe 2-3 minutes. I think the #20's are a great idea!

should take the same time as before, 20s are no imporvement for faster starting warmup time, you have to use the choke or  you are too rich at idle and seems to run better while it is stil cold.

only way to know how "warm" is the engine is to touch the crankcase
a gs with 2 minute is cold, always. you have to warm up 3 litres of oil first.

my bet is it is too rich, with 20s you should close mixture screws a bit for same amount of fuel

Full choke should idle high when its cold. Yeah like 4500 - 5000 rpm. Totally warm GS takes like 10 minutes of riding. If you just mean warm enough to take the choke off, then yeah bigger idle jet will let you take the choke off earlier at the expense of wasting a little fuel the rest of the time. Its like always leaving the choke on a little at idle. Better to just deal with the long warm up time and get better fuel economy.  Its not a bad thing for the bike to need choke for awhile, that's how it was designed to be used.