I had a top I had all sorts of problems with the tucks and such in the back. I was using my vintage small throat machine and even though I did pick out some of my quilting and re-quilted I still had some huge "pookies". It's one of the reasons to pick a print back as opposed to a solid, but after I had taken the stitches out once, the next time I just sewed the bad tucks down and ignored the small ones. With the print you couldn't even tell.
With fleece, maybe a bit more problematic but again, you are making it with love for someone who loves you and will love it in return. And keep in mind, unless they share the hobby they don't know what perfect is. Even if he did, as you said he will love it anyway.