I can't comment on your fuel consumption question, but definitely, if you are drawing 100 amps of your alternator when underway, you have less power available for propulsion. If you have the alternator engaged, but less draw on it, i.e. batteries full, or fridge turned off, you will have more power for propulsion.
Probably only noticeable if you are trying to confirm max speed in flat water with a clean bum. Normally there are so many other variables you would never notice, like chop, wind direction etc.
When we repowered we went to a fractionally smaller engine, and I was very keen