Paper is not flat in regular easles either. The neg not being flat is most likely the problem. Use a grain focuser center and edge and if you have a good flat field lens and the negative is flat, the grain will be sharp corner to corner. Align the enlarger as required.
Negatives are only flat with a glass carrier. a top glass will get you 90% of the way. Double is 100%.
I align the my enlargers with a Peak grain focuser, long mirror, that goes into the very corners. I am sure lasers and mirrors are better, but if I can get sharp grain corner to corner with a wide open lens, I call it good enough. The short mirror Peak will not get into the corners
My D2 is alligned with a 50 mm lens on a flat plate. 135 or 150 lenses on the proper cones are shimmed to be be perfect. Allignment is never perfect across the different lens cones and lenses. Strange but true.
My leica enlargers are perfect and never need alligning. The 4x5 Omega D2 and D6 reguire a lot of work but make perfect prints once they are set up. The Phillips models are fair. I use it for the tilting head and neg stage for perspective correction.
Paper is only flat with a vacuum easel. I never needed one because I do the first steps correctly. But if you want absolute perfection, that is the way to go. Do all the first steps first or you wasting yout time with a vacuum easel.