I think it makes sense for some Pokemon to be weaker than others. In terms of game balance, weaker Pokemon need to exist during the start of the game so that the player isn't utterly crushed by repeated encounters. They definitely have their purpose in games, and boosting them is a risky move. If you hack forced a situation where the starter was non-standard and had much higher bases, then boosting would be fine imo. It's a little unexpected, and not really a practice I would recommend. Giving boosts could be done in the form of movepool tweaking and other smaller changes like exp rate. Atleast, that's my view on the situation.