You have already 'deep clean' the toilet and the stain is still there. I guess normal cleaner won't work. I suggest cleansing agent that labeled as 'concentrated'. Another good way is to use hydrogen peroxide.
I google the website and there are nice tips here
How to Clean Tough Stains from a...
From the picture I doubt it's mold. I'm pretty sure that it's just inner part of your carpet.
Just flip up the carpet and see what's happen.
About the possibility that it would be mold. Don't worry too much.
Mold is not that dangerous of you don't eat them.
A normal fabric face mask is...
The patch isn't the problem, if it's properly place it'll be there for a long time.
The real problem is the cause of crack. If your floor crack because impact from usage, the patch should OK until it gets another big impact.
However, if your floor crack because non-uniform...