When I did my bathroom I took up the toilet, laid the new vinyl and replaced the toilet. Not that difficult.
I read somewhere, that you make a paper template around the toilet then transfer the template to floor tile. It should fit like a puzzle piece. Good question, I was also wondering the same thing. Good luck.
It's been years and I'm sure there is an easier way...but I laid newspaper down and make it fit around the toilet (rubbed it down) and the trimmed it to fit just right. Then use that for your tiles!
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