Many thanks for all the opinions so far... much appreciated!
Based on your responses, I'm now leaning towards just leaving the Johnson and Young cards as-is. I don't want to get caught up in the re-submission game, as it really only benefits the TPG. I do firmly believe the Cy Young should be a "4" but perhaps not worth going through the hassle of cracking and re-submitting.
Yes, the Walter Johnson has a slight diamond cut, but I have other cards with equal or more severe diamond cuts that are graded 4, 5 and even 6. Probably because they were graded a few years back, when the standards were looser. There is a faint stain on the reverse side... perhaps from contact with tobacco. You can barely see it in-hand, but the still photo above really accentuates it. Perhaps that factored into the grade as well.
I have no issues with any of the other grades... the T206 Waddell portrait is trimmed and properly graded. And if anything, they were somewhat lenient with the Fred Clarke CJ and the Ed Walsh Portrait.
Many thanks to all who provided feedback, as grading "ain't my bag, baby" and I consider this very helpful.