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If these are second hand rods then my recommendations change but just a bit. This appears to be a simple asymmetrical resizing of the big end. I'd have them all double checked again perhaps by a different shop or machinist to ensure they're truly round. Whoever handled the resizing cut a bit more from the cap side than the rod. If you reverse the bearing - take cap side and put it in the rod and rod side and put in the cap - does the gap stay in the same position or does it move with the bearing half? For the rod side of the bearing shell to move some significant deformation would be occurring which I find hard to believe.
The concern of compression height is if the center of the hole is now slightly different on the big end. This translates to different finishing piston altitude at the top of each stroke. The difference may be minute/negligible but knowing that it's moving I'd still keep an eye on it.
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“Of the value traps, the most widespread and pernicious is value rigidity. This is an inability to revalue what one sees because of commitment to previous values. In motorcycle maintenance, you MUST rediscover what you do as you go. Rigid values makes this impossible.”
― Robert M. Pirsig, Zen and the Art of Motorcycle Maintenance: An Inquiry Into Values
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