And all that heat is wasted energy. In other words that saps some of the power from the bike. Alternators, like intake systems, have to be right sized. For example a tiny alternator may be fine on a drag race bike where the rules say that it must have a charging system, but would be useless on that same bike on the street.
A 350 watt charging system on a bike that never needs much more than say 150 watts is wasting power at most speeds. The odd exception is if a charging system has insufficient output at low revs and that bike is usually run at low revs, then a larger alternator might be a good fix, even though it would waste power at revs the bike rarely, if ever, reaches.
Sometimes a slightly larger battery and small stock charging system are a better fit. It's all about getting the right combination of parts for a particular application.