I have a theory, and it's to do with responsibility. The maintenance bypass is make before break, and thus the output of the UPS (in the sense of the UPS as a 'box') is placed in parallel with the line. With an internal UPS, it's easy for the manufacturer to ensure that there is interlocking to make sure the UPS is in static bypass mode before the manual bypass is connected. If there is just an external manual bypass, the manufacturer has to rely on the in stallion electrician to configure additional contacts on the manual bypass switch to do the interlock, or to reply on written instructions, or castell keys, all of which can't be the manufacturers responsibility. If the UPS is in invert mode rather than static bypass, and in particular is not in phase with the supply at the moment of bypass, then the manual bypassing may be not so smoke-free.
To be fair, for most repairs to UPSs you can internally manually bypass them ands then once the isolators are thrown almost all of the gubbins can be worked on freely with no risk of shock. Obviously the switchgear panel is excluded from that 'most' statement.
