I don't know how to summarize my problem any better than in my op.
I don't understand some of the discussion from Phill Lockhurst and gmc, so it's hard for me to clearly understand what they might or might not be on to. So I apologize, but I can't clarify their discussion for you.
Maybe you could read through my op again, and for the moment, ignore their discussion. Maybe it will be more clear that way? If you don't understand my op, please feel free to ask.
(Still waiting for my new isp to take over. Good chance I'll lose my connection any time now. But hopefully I'll be back soon, whenever it happens

)
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In case it matters. And for the part of their discussion that I do understand:
For gmc, I've created a 2nd temporary album (
http://inkscapecommunity.com/ic_gallery/thumbnails.php?album=28) and uploaded Phill's lower bit PNG as both the original and the custom thumb. The original appropriately displayed the bg, before the custom thumb was applied. And it still is correct bg after custom thumb is applied.
However, it looks like Phill had taken a thumbnail from my album, rather than the full size PNG. I'm not sure if it makes for a fair test, to use a thumbnail. I guess if he took it from my PNG original, it should be fine. But if he took it from one with the black bg, it might not be good to use for testing.
Even though Andre said it should not matter whether the original image is an SVG or not, I still wonder, based on my first experience (memorialized in the linked reference topic above). So in this 2nd temporary album, I uploaded again, my original mand2.svg. Then I applied Phill's low bit PNG as the custom thumbnail.
You can see, that even though I used the same PNG (Phill's low bit) as the custom thumb, on both images, Phill's low bit PNG as the original shows a correct bg for the custom thumb, and my mand2.svg as the original shows the black background.
So I learn 2 things from this:
1 -- The Custom Thumbnail plugin
does behave differently when the original is an SVG.
and
2 -- The low bit color does not fix the problem.
This is only valid if Phill's low bit PNG came from my original PNG upload. If he took it from one with the black bg, might not be fair test.