According to the wiki:
spoilers
Before going to the last mission trigger, it is advisable to complete any remaining side-missions, etc. that may be required for 100% completion first as, depending on the player's choice, Michael or Trevor may no longer be available beyond this point, thereby rendering any activities/side missions specific to them inaccessible (even though their missions are not required for 100% completion). If Michael or Trevor possess any rare vehicle the player doesn't wish to lose, cars should also be exchanged before starting the final mission. Unless the player has already completed everything else (except Lester's assassination missions and other Franklin-specific sidequests), they must be careful not to take Franklin to his safehouse so as not to trigger the endgame.
answer(possible spoilers)
"even though their missions are not required for 100% completion".
So yes it is possible to get 100% completion with ending A or B. It doesn't matter which ending you choose. Because you can't play the side missions after you killed one of them, you might want to complete them before you kill the character.
