From my perspective as a former N-V engineer with significant involvement with the Commando, I wouldn't risk drilling holes in the top tube , even close to its neutral axis, but particularly not at either the top or the bottom of the circumference. Stress cracking would be a major risk, even on the bikes with the secondary reinforcing tube.
I had an interesting experience with the AJS moto-cross bike, which had a very similar frame design, though with the top tube attached at the bottom of the headstock rather than the top. We had done very well at one particular race meeting. Dave Bickers asked if he could try out the bike after the races were over. He did a number of very fast laps and was very complementary about the handling. Back at the factory, we started our usual post-race strip down. When we took the gas tank off, the frame fell apart. The top tube had broken into two pieces just aft of the headstock.
The frame was redesigned by separating the top tube along its length into two halves, then welding in a long skinny triangular steel filler. This made the tube obround at the headstock end and circular at the back of the seat. We had no more problems with the frame during my time at N-V. I suggested to the folks at Plumstead Road that the same fix would solve the Commando issue, but they said it was too much trouble and went with the secondary tube design. As far as I know, all the production AJS Stormers were built with that redesigned frame.