If Subeta can autoprice things too low, which apparently is the premise for the undercut argument or one of them (I'm not fully caffeinated yet and this thread is bordering on a tl;dr), why not have it that Subeta also automatically pulls these items that are under a "certain value" and puts them back in the inventory?

"Oh, we can't do that because database and coding." You're pulling fluctuating prices off the site on a daily basis for hundreds of thousands of items at thousands of random intervals during said day, I think it's semi-plausible or at least should be considered before being dismissed entirely.

I undercut by accident because I'm not going to scroll the length of my shops with even a couple thousand items and make sure that I'm not undercutting someone by 1sP, 10sP, 100sP or 1000sP. You get the idea. But because I'm not as thoroughly checking things as some people, I'm public enemy number one.

Options to flag you for large changes on items priced above a certain sp amount might fix some issues.

Say -50% -7$% and 10,000(maybe) 100,000 1,000,000 (just examples)

So you pick the first option on each. Any items that -were- priced over 10,000 that drop by more than 50% would either move to the top and be highlighted or have a separate 'warning!' page. Anyone who doesn't want to deal with that doesn't turn on any options.