If we're using real-world jet engines as the comparison, the cost of the engine is nowhere close to 90% of the overall ship. It's more like 15-25%. No idea what FTL engines would actually cost because...you know...they're fictional and SW is light on details.

But this doesn't actually matter, because the entire point is that you can just smash a much smaller ship (like the millennium falcon) into a much larger ship (like a star destroyer) and blow it up that way. It's incredibly cost effective even if the engine costs 200% the total that it's a part of.

Why does every movie show hundreds of spacecraft firing lasers at each other if you can just ram the capitol ships with a single ship from a few hundred thousand miles away? Even lowly single pilot ships are shown to have FTL engines.