You'd expect for any kind of proper reman they'd routinely check bearing/bushing wear for freeplay and smoothness. Perhaps it checked out, or at least barely. You'd also expected them to spin it up when they're done and check for full output, which hopefully would catch a noisy bearing, but perhaps the shop was noisy. It's hard to trust remans some days. It's hard to trust ratings. The reman shops may normally be good, but may be inconsistent if they don't pay attention to quality control. I prefer my local alternator/starter shop to do re-builds, but of course it takes longer unless they've got a core exchange on the shelf.

If you're concerned that dirt and/or water could get into the first alt through those broken spaces or the windings could otherwise get damaged then something like JB-Weld may be up to the task as a filler. It wouldn't have to be level except for looks. JB-Weld contains iron particles as I recall. I would then consider using a backing filler first, something non-conductive, perhaps a scrap of styrofoam, to avoid having anything conductive on the windings. Other epoxies wouldn't need it exept to save on amount used.
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Dave -still with 940's, prev 740/240/140/120 You'd think I'd have learned by now