For some strange reason I decided I wanted to refinish the scatter sheild and block plate on the truck before I put the engine back in it. I glass beaded the parts today with the intentions of dropping them off for powder coating tomorrow. I'm now having second thoughts about it as fear of surface irregularities dance through my head. Part of me thinks I'm making mountains out of mole hills but another part of me is afraid of creating a whole new problem to deal with. So with the exception of the dowel holes and the center hole for the bearing retainer do I need to worry about the mating surfaces? What says the experts? Move forward with powder coating or stick to paint?

The powder coating shop will have high-temperature masking tape, and plugs, so they can mask off anything you need.
I doubt a few thousandths of paint on the block mating surface is going to hurt anything. The dowel holes are a snug fit by design, so block them off... ditto the threaded holes.

Do either of these items need to have a SFI certification?

It should be fine. Verify your results as a standard operating procedure. If needed it can be milled to square it up.

I have a friend/customer who was having issues dialing in his stock SB bell housing due to paint on the bottom part where it bolt up with the two 7/16 bell housing retaining bolts. He wasn't using them when dialing in the bell housing and ended up .015 run out wit the max offset dowels he could buy, he installed and tighten up those two bolts and ended up wit. 003 run out
I'm thinking no powder coating on any of the bell housing to block mounting surfaces I wouldn't coat those surfaces
I know of other guys on here who have indicated the tranny mounting surface on their bell housings and scatter shield that found that surface not perfectly aligned with the block mounting surfaces causing pilot shaft to the pilot bearing problems

Brand new the mating surface comes powder coated on the bell housings.
Powder coating goes on as a thin even layer, I would not worry about the surface of the scatter shield
as it will be bead blasted during prep prior to coating.

Some are, some are not. As we say trust but verify : D

I'd be more worried about distorting the bell housing with the heat from the oven than the .0015 thick coating.

Powder coating oven only goes to 350-375 then slow cool, I would not expect any movement of the material.

Most plastics, powder coating is plastic sprayed on and then melted, don't conduct electricity so the tranny may not be as grounded as good as it could be which may add to electroiysis interaction between the motor and tranny That is not something I want to happen to any of my parts on my toys or any other vehicles

Maybe the powder guys around here aren't doing it right, but on the stuff I've had done and seen, the coating is multiple thousandths of an inch thick. A corner gets bumped and chipped and the stuff ends up flaking off. Holes need to cleaned. Threads chased. Mating surfaces need to be cleaned. Stuff needs to be ground off to restore slip fits. It's a PIA to get cleaned off well enough to weld a bracket or part and/or do a weld repair. Not to mention the media blasting that has to be done during prep and the problem of getting that crap cleaned up. I've seen expensive assemblies eat themselves up because they weren't cleaned properly. They were pretty, but they were still ate up junk.

I have stopped doing powder on anything that has been fitted during fabrication and has close tolerances and fits. Or is something that is best to not use abrasives on that may cause future problems - rear housings, engine components, trans cases, etc. I have better results with things being properly prepped and painting, even when that involves me doing the prep and using Krylon.

After going back and forth, I finally decided I would be the test dummy and went ahead and dropped the parts off for powder coating this afternoon. The guy I spoke with said the coating would be around .002 thick so surface irregularities would be minimal if any. He also said they would plug all the threads and mask the bearing retainer journal as well. I did consider the grounding issue with regards to the starter specifically but concluded that either a ground strap to the transmission would suffice or depending how it dialed in, possibly milling / removing the coating from the mating surfaces as a back up plan. Disclaimer... I did not check to see how well it dialed in previously as it was already on the truck when I bought it. I will however report back with an update on how it goes when I reinstall it. Hopefully it goes smooth, realistically it'll be frustrating, worse case scenario, it goes in the garbage. Let's hope for the first one.

I hadn't thought about the starter being mounted to the scatter shield when I made my post on grounding, you can run a ground from the frame to the starter upper mounting bolt to help ground it
I have done that on several cars with the battery in the trunk

I have my scattershield powder coated. I also run a ground cable to the starter, hooked to a dedicated ground location. One issue I had during assembly was powder in the input bearing retainer location. I had to sand that down to bare metal so the retainer would fit the opening.