Putting it over HTTPS won't necessarily stop them. The caveat mentioned in the article is that they won't track your HTTPS web browsing. But they can still slow it to a crawl if they don't like you doing it.
No worries! Actually I wonder if just tunneling over TLS would be enough if the ISP were determined. I mean, after they see me pushing and pulling GBs from the same host for an hour, they might just GET it themselves. If they see a "how to configure your VPN" page, that address could go on a slow-list.
Yes, you could tunnel VPN traffic over an HTTPS connection. I have built VPNs using ppp over ssh tunnelling before, and that works fine.