[EricH]

Take out the "possibly" part of the rule violation. I quote the rule, with emphasis:

R33
The integral mechanical and electrical system of any motor may not be modified. Motors, servos, and electric solenoids used on the ROBOT shall not be modified in any way, except as follows:

A. The mounting brackets and/or output shaft/interface may be modified to facilitate the physical connection of the motor to the ROBOT and actuated part.
[Parts B through G do not apply to the question.]

The way I read what you want to do, and the rule, you are proposing modifying a part that is neither mounting bracket nor output shaft (part of the motor case, in fact), to facilitate the connection of an external device to the motor' s output shaft, which is not covered under any part of the exception list, and which is therefore illegal. You might be able to argue the intent with one inspector, but you probably won't be using that motor once you hit the LRI, and almost certainly won't be if they happen to call Big Al. Unless, of course, you can get Q&A to specifically allow that sort of use, but that's kind of a long shot (my prediction of their answer ranges from a straight "No" to "Rule R33 does not allow that because...").

The intent part--the way I read that blue box (which, BTW, is NOT a rule, just a clarifying statement) is that the exceptions are allowed for "ease of use"--mounting to the robot or whatever the motor is moving--rather than "we think we can do this without violating the maximum power rules".

Now, that said: Why don't you, instead of drilling and tapping the back of the shaft, drill and tap the other end? Most gearboxes I've seen don't block that from being accessed. Add your encoder to that end--you may need a plug or something to adapt it--and you should be OK.