@mmat1 - in the next beta release, well formed checking cannot be turned off and hence the option has completely disappeared. However it also is only triggered when it absolutely needs to be rather than every time the window loses focus like it was in Sigil 0.5.3 and earlier. You can for instance switch into Preview View without triggering it, switch tabs etc. What *will* trigger it is attempting to switch into Book View, saving, or doing any actions which require some sort of saving behind the scenes (like splitting, merging etc).
As for the Regex options, yeah there is some history behind it. The original 0.5.9 beta had no Regex Dot All option at all so that those options were included in Sigil anywhere at all I considered a huge win
. Personally I have been using this Sigil codebase for three months since I added them and not once have I found a need to turn any one of those three options off. So as set and forget it hasn't bothered me to not have them anywhere else. But clearly my usage differs to yours. As always it is a question of the how and where without making it all look too confusing and busy.