What does this warning mean
It means what it says - any conversion to CMYK may yield a drastically different color result. unless you are 100% certain it actually gets printed with the colors you defined at the given densities, you may want to dig out your pantone swatch and find substitutes that giver the same coloration without relying on transparencies, as clearly would be preferable for package printing under most conditions.
This means you have colors that are specified as spot so the would in print separate in an ink other than the process of combining CMYK. Though printing for example a spot color of f field of PMS 320 at 50% is nto an issue, a problem occurs when you have for example a blending mode as that spot has to be converted to CMYK, in the conversion there will likely be innacuraccies.
If you need more help please provide screens shots of your individual separations preview for each spot color you have. Windows >. separation preview is some I recommend you like into to explain what is going n here.
Check the separations preview to see if your spot colors are still separated as separate plates.
Thank you - this simple explanation, made it clear what I was missing. It's my first time designing packaging in Illustrator, and I wanted to make sure I understood all the warnings.