My EM plates are different on both sides ( CVH 1.8 engine) , 1 side is flush with the bottom rails as you describe & the drivers side has a 30mm rise, this is to facilitate fabricating the engine mount to clear the steering column on this side.
Its ok to make the EM plates flush with the bottom rails ( subject to fabricating the actual engine mount heights), its the engine mounts that create the height of the engine & the sump clearance you require for your given engine.
I hope that makes sense
cheers
andy