Various ideas here. 1) That your feet now don't sit identically - doesn't surprise me. I'd work on getting each foot/leg to the place where it is at its best and let the symmetry or no be what it is. But watch for issues cropping up from the asymmetry. Your body will be the best indicato of what works. 2) Consider all the options. You may well want different pedal types for each leg. A pedal like the Look Keo can be used with different cleats with different releases and on many clipless, you can adjust the release resistance. I use the same pedals left and right and same shoes but I have the right show toed in by the cleat a lot with the left shoe nearly straight. Run laces on my shoes and lace them completely differently. Odd but it works. If I set them up symmetrically, rides and after would be painful and at least one knee would be up for TNR. As is, I've staved off that TNR now for 45 years and hope to go a few more. If/when it happens, I'll have to follow the advice I" am giving you,
If you are one who puts his right foot down; so the TNR leg stays on the pedal, consider an old fashioned toeclip for that side. No twisting at all. You can ride with the strap loose enough to always be able to pull your foot out or reach down and pull it tight and it is fully the equal to clipless. (But you do have to remember to release the strap or you fall over when you stop. Now it you just relax and accept that you just made a fool of yourself.very little happens other than a couple of minor bruises and some slightly dirtied clothing. I've been riding with toeclips 50 years and I still forget. If your TNR leg is also your "put down" leg and you want to go toeclip for it or both, get back to me and I"ll pass on tricks to make the toeclips easier to get into.