There shouldn't be any negative impact on you when the lease is up. As with any other warranty repair, or even professionally performed body work.
The competence of the repair shop is my sole worry. I have no reservations about taking my car to a reputable body shop in my area for a respray. They may be able to achieve an even more precise colour match than the factory when painting metal panels and plastic bumpers. On the flip side, though, terrible painting... Perhaps things won't improve much from where they are now.
The repair shop is up to you when it comes to collisions. However, how that relates to the paint defect warranty repair is something I'm not clear on. Must it be a particular store? Does any store belong to the "Mazda Collision Network"? You might also try selecting a store and getting their stamp of approval. Seeing the shop and their work is a must if you have the chance. Most reputable businesses are pleased to show you their office and the finished products because they are proud of their work. (If you give a general area, maybe you'll get some recommendations for stores that people here are familiar with.)
Concerning the inquiry as to whether or not other people are experiencing the same problems... The CX-90 in our driveway is the only one I can speak for, but the paint job is amazing. As far as I can tell, it is flawless and devoid of any flaws. Reflections barely show any waveform. The painting is of exceptional quality. However, their vehicle production is in the thousands. On occasion, some will inevitably experience problems. It might be related to surface preparation or contamination in your situation.