These are some my opinions to the questions you've asked.
1) Is using the removal tool to remove the whole site the same as using robots.txt to ban Google. If robots.txt is a low-strength medicine is that preferable i.e. ban googlebot, all google crawls stop, google stops showing your page, you re-allow Googlebot, it re-indexes, you've lost a few days traffic but have now got all your pages indexed and indexed correctly. (It can't be that simple, can it?)
Disallowing Googlebot doesn't remove your pages from the index, while both disallowing and removing the site with URL Console... also doesn't remove your pages from the index, but hides it for six months. There is no way to remove pages for a few days and then get them back. All you can do to clean up your indexed pages is to set up proper 301 redirects and keep waiting.
I succeeded to clean up some URLs with 301 last month, so 301 are not completely broken.
2) What do you do if yoursite.com/index.htm is a duplicate of www.yoursite.com/index.htm. OK, you've got your 301 in place but how do you treat the removal of the index.htm page?
Use 301, and ensure that wrong URL also has some backlinks so it's likely to be crawled. Take care to have much stronger backlinks to right version.
4) If you use the removal tool and remove your whole site for a while... when your site comes back do you still benefit from all your backlinks? I'm assuming that removing your site from Google's index is not as serious as allowing your domain to expire :)
You benefit from your backlinks even during the time period when the pages are removed - Google keeps crawling them, follows outbound links and credits PR to them.