See Seafort's post, with emphasis on the word "shoehorn." The issue isn't the size of the core, it's the size of all the ancillary equipment that is integral to the M/AM reactor. Yes, the core is only as big as indicated on the MSD Sonic provided; but the majority of the whole engineering hull is control and diagnostic equipment, reactant storage (fairly important and rather large,) etc., etc. So...
#1 - Do you really want to keep huge tanks of the most volatile reactants known to man aboard the "safe" part of the ship, the part that's supposed to be an escape from danger?
#2 - Even with a reduced-capacity core, all that other stuff needs to go with it. I think a lifeboat limited to impulse is a better option than a warp-capable lifeboat that can only take one-third of the complement.
#3 - Even only discussing normal operations, what do you have to sacrifice to get that warp core et. al. into the saucer? Yes, the arboretum, patisserie, coffeehouse, and whatever other "space-hotel" crap can conceivably be dispensed with (but see below;*) but if it comes to taking out stellar cartography or research labs or somesuch, you've succeeded in negligibly improving an emergency function at the cost of sacrificing part of the ship's primary function.
* - Even though we all laugh at the type of amenities that a GCS apparently has, they were put there for a reason. We are talking about people - civvies, not just Academy-trained crew - who are going to be aboard for long stretches at a time. The people who designed the GCS were obviously not willing to dispense with those things, presumably for reasons that behavioral and competency research had shown them; therefore, binning those amenities isn't an option, even if you feel like sticking a
powder keg spare core in the saucer.
"We've been over this. We don't shoot first and ask questions later."
"Of course! We never ask questions."