we have a 496 mag and the boat run 61 mls
we changed cam to HO and the boat runs 64 mls with the original mag computer , then we changed computer to 496ho .
still excact the same speed 64 mls , so is there realy a difference between mag and ho computer?

I dont think there is too much more timing advance if any. There is 100 more RPM on HO stock spec than mag.

Send the computer to Whipple to get Stage 3. It is a lot better than stock.

50 hp increase and a 3 mph gain is right what it should be.
Not sure about the difference in tunes, but You were probably lean with the stock mag tune and are probably a little rich with the stock HO tune.
Sending it to Whipple for a performance tune is probably good idea if you want to get every last mph.