Does "perfect alignment of cart" eliminate 100% ?

Be realistic. If you can hear a problem try to sort it - if not, leave it alone and listen to music. If you can't hear a deterioration then you are OK as the stylus will be operating within its tolerances. If you do, then you can try altering the alignment - simple.

If you're talking about it happening on many records, then your cartridge setup needs work. If it's only on one or two records, it could be the recordings or your specific discs.

There's no such thing as perfect alignment. All alignment tools are approximations only, and their accuracy varies as the cartridge sweeps across the record. Furthermore, the thickness of the vinyl influences the geometry somewhat and varies from LP to LP, so unless you are prepared to set the alignment for each LP, you might as well leave well enough alone.

Cheers