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Perhaps some clarifications can help ...
- The URL removal tool is not meant to be used for normal site maintenance like this. This is part of the reason why we have a limit there.
- The URL removal tool does not remove URLs from the index, it removes them from our search results. The difference is subtle, but it's a part of the reason why you don't see those submissions affect the indexed URL count....
For large-scale site changes like this, I'd recommend:
- don't use the robots.txt
- use a 301 redirect for content that moved
- use a 410 (or 404 if you need to) for URLs that were removed
- make sure that the crawl rate setting is set to "let Google decide" (automatic), so that you don't limit crawling
- use the URL removal tool only for urgent or highly-visibile issues.