Sounds like a good plan depending on how long before you add on. Your boiler will probably short cycle which will shorten its life. If there is chance you wont add on its a little risky. You could do the smaller unit and plan on making the addition super efficient.

I assume this is a hot water system and not steam.

I am a homeowner and not an expert, but you have to be careful about matching the size of the boiler to the amount of baseboard. You should discuss with the HVAC contractor how this will affect the performance.

I suppose you can think of the extra manifold being connected to a separate zone which is never enabled.

Boilers have long lives, so I would not be worried about reducing it. I grew up in old houses which had oversized boilers. They seemed to last forever.