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I totally agree with the urge to keep document files in the same repository as the code.
The only downside I have seen to running your own documentation website is that you have to run a website. That said, if all you're doing is hosting a bunch of auto-generated pages, there will be a bunch of up-front work to set it up and then sporadic bursts of work when things break, or it gets hacked or whatever.
I'm pretty sure that doing a subdomain is just a matter of 1) running a webserver on a computer with a static IP address and 2) getting the (super-)domain owner to add your webserver's address into their server configuration as a subdomain.