Are you saying Y is just 5 cm higher than 3 ?
No, you're reading too much into that. 5cm is just the amount of raising you can do on a Model 3 practically as a "freebie" - just some extra spacers in the suspension. There's some parts that need to be longer (I forget which ones) if you want to go higher than that. Said parts are surely among the ~24% of parts different between Model 3 and Model Y.