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I've been designing a typeface on Fontlab and been running with this problem, let's take the "#" glyph, to design it I made two vertical shapes and two horizontal ones, they look perfect when unmerged but as soon as I merge them their alignment gets all messed up:
To solve this problem I've increased the size of all my characters, went from 500 height to 1000 height and this kind of problems started to disapear since now I have much more space to move the points around, there's still some unaligned lines, especially the curved ones in complex characters but I've pretty much solved it.
My question is, is it fine to have a typeface with such high height? Will people run into any render problems when they use it?