Is it a bad practise to have the same website in more than one listing (the NAP is different) ?
Like Phil, I'm not so sure we are clear on the situation. Please explain more.
Same company, more than one location, just different address and phone???
Yes use same site, but if possible a location optimized landing page for each listing, that has uniquely optimized content. Check the tag cloud button on top menu and look for #multilocation hash tag.
If you mean something else besides a multi-location company, then please explain in more detail.
Would you just add the specific location URL in the website field in GMB or just the website main URL?