We had someone come in with a hollowtech BB today. We have the BBT-9 at the shop that we used to remove his old BB, then he wanted to install a new hollowtech BB, but the new BB had a smaller diameter. We were super busy so I didn't get a good look at it, but all I knew was that we didn't have the tool to install the new one, and we didn't want to go at it with a pair of channel locks.

It seems that I can find 3 types of hollowtech bb diameter. The normal one is 44mm, then the other park tool has diameters of 39mm and 48.5mm (double sided tool.) Are there any other common sizes we should get the tool for now or do those 3 sizes cover it?

Is it safe to assume all the bottom brackets you're talking about are Hollowtech II? Hollowtech (I) cranks used Octalink bottom brackets.

For outboard bearings in general, including Hollowtech II, there's at least one more size in addition to the ones you mentioned. Shimano Ultegra 6800 is 41 mm. But those bottom brackets come with an adapter that lets you use a 44 mm tool.

The newer Shimano BB's, that I have installed, come with a plastic adapter in the box.

Yes, it seems you are correct. I'm obviously not particularity familiar with the technology!

Yep, just did one last night. Had to use a vice to get the plastic adapter to seat fully in the tool but it worked fine.
A bit fiddly to keep it straight while I torqued it, the plastic makes the tool longer and must have a bit of give.

+2. This has been the case since these latest generation Hollowtech II bb's with the smaller cup diameter were introduced, which has been at least two or three years I believe.

Did you put the adapter on your BBT-9 in the correct orientation as shown in the little manual that comes with the BB? I initially had my adapter turned around, but it worked like a charm once I fixed my mistake.

No, I was using a full socket type, like a BBT-19.2. It's odd, the BB didn't come with any real instructions, just a piece of paper in umpteen languages with the "naming of the chainwheel parts".
I had to Google to confirm the proper torque.