Pin numbers in Decal Editir are fixed size. Please to to Merntor Ideas and file an Enhancement Request.
I've had login/email problems, so I apologize for the long delay in answering this question, but I wanted to go ahead and get an answer in here...
There IS a way to re-size the Terminal numbers in the Decal Editor. Including for the wizard, but it isn't intuitive. You just have to change the Pin Numbers Default in Tools-Options-Drafting before building a part or using the wizard. At least this appears to work when I tested it.
You can also do this after the Decal is built, once you've OK'ed out of the Wizard.
Note that if you change the default, it will stay that way until/unless you change it back.
It still does have an incredibly annoying bug though (at least as of v9.3.1) - The Reference Designator text will also come out the same size as the Pin Number text. But that's easily fixed once you finalize out of the Wizard.
This is a LONG-time problem in the Decal editor, a separate setting for Pin Numbers and Designators, so that they will come out as different sizes, has been repeatedly asked for in the past both on the Ideas site and before that site was started, through submitted SRs as a request to fix this bug. Doesn't make any sense, at least to a layout person, that the same setting controls both the pin number and designator text.
Wanted to give you a big THANKS! for the answer to the terminal number size. I created a BGA footprint last week, and I was wishing for a way to reduce the number size. I'm going to make changes to several footprints.
Thanks so much John!!!
Its a shame you can't change in independently for each footprint but it's better than no flexibility at all!!
Just out of curiosity, why don't you just turn off the pin numbers while you take care of the rest of the decal?