This is a difficult and controversial question to answer. Van's does not give much guidance and did not leave much in the way of natural routing even for the battery, elevator trim, and tail light. Anything more and you are forced to make additional penetrations - at your own risk. Since we know that many RV-10s are flying with additional equipment in the tail cone (pitch and yaw servos, remote ELT, antennae, air conditioning, etc.) then it appears that a certain amount of extra penetration is not immediately harmful. Just don't get carried away.
The problem with penetrating the F-1005A is that you must immediately make a 90 degree turn to stay under the flap actuator covers. Generally, you prefer conduit as straight as possible to avoid problems feeding wire into it. I ran my AHRS cable through the left side because my AHRS lives under the passenger seat, so I only needed conduit through the sidewall. On the right side, my conduits (and A/C hoses) continue through the sidewall to penetrations I made in the baggage bulkhead.
On the left side I had to drop my conduit through the baggage floor before reaching the baggage door, leaving an undesirable vertical S-turn in the conduit. A better option might have been to penetrate the seat floor instead, as well as the first F-1017A, before passing through the precut hole in the next bulkhead, allowing a gentler, but still not straight, transition. Sometimes there is no perfect answer.
When the lift my project was on failed, the fuselage skins were wrinkled behind the main spar - it was that hard a drop. But removal of the skins and examination of the structure underneath showed that the areas where I had made additional penetrations had stood up just fine. That's not proof, just anecdotal evidence, but I will feel better once I've got the new skins back on and eventually finally complete the aircraft.