Yes it is safe and acceptable to shoot lead through a Mag-Na-Ported revolver.
As mentioned some lead will come out of the ports and adhere to the sides of the sight base and blade.
Back when the Smith & Wesson Model 41 was a restively young design (60s/70s), many of us bought the 7 3/8" barrel with the V-comp
The comp worked very well at speeding recovery times from shot to shot, but that V-comp used to get clogged up with lead . . . after all we were shooting 22LR
It was bad enough that some impatient folks even used dental picks to get it out. Then Gil Hibbard showed us the light. A quick spray of the V-comp with Carter's Compensator Cleaner and the lead almost all wiped off with a rag at the end of the match
Well Carter's is gone today, but the concept is easily replaced with other products. A quick blast of Hornady One Shot case lube works almost as well at keeping the lead from adhering to the comp. Plus there are lots of others that will work
As to the BIG X-frames, at least the 500s (never owned a 460) the second comp insert had all the same ports except the ones facing the front sight. Personally, I never bothered changing any of mine