Ok.. after further work on my testbed 10.10.5 system here..
I can confirm they have now apparently hardwired the Letters to the Tools... so you cannot change them
You can get the ESC to work but not reassign numbers to the tool commands themselves...
No idea why.....Maybe a report via the feedback form would be a good idea...
https://www.apple.com/feedback/logic-pro.html
So at the moment, you can either try rolling back to 10.2 using your backups or...get used to the new system...
Cant think of any other fix given the apparent hard wiring...
Note: I tested out the older LP9 key command file and the same behavior is now noted after updating to 10.2.1 so that doesn't help either.