Another vote not to notch it. The structural and glass work sounds complicated. Closing a transom is adding structure and strength. To cut away structure and then engineer it to restore strength is much more difficult.
You don't have to have a full 28" bracket. Just MacGuyvering off the top of my head, you can use a setback plate maybe 7" or 9", like one from Cook Mfg. (
http://www.cook-mfg.com) Or a mini bracket from Stainless Marine (
http://www.stainlessmarine.com/prices.html). It only needs to be long enough to provide clearing for the steering arms and rigging. Even if you have to drill a new hole for newly routed rigging, it'll be high up on the transom above the waterline and way easier to reinforce than a notch. The added length between a setback plate/mini bracket + conventional outboard, versus your current SeaDrive might be what, 4" tops? I can't believe anyone would notice, let alone boot you out your slip for it. Just my thoughts...