It seems that all that's missing from the mobile view is the actual flag link: if you use developer tools to inject an
<a class="comment-flag"> element somewhere inside the comment row and click it, a seemingly functional flag dialog pops up. (I haven't actually tried to submit an actual flag that way, but I see no obvious reason why it shouldn't work.)
Thus, it shouldn't be hard to write a user script to do this — the only problem is the lack of user script support in mobile browsers (Tampermonkey browser notwithstanding).
(In fact, the reason I noticed this is that the code SOUP uses to work around this issue is currently (v1.8.0) missing an
isMobile check, and so ends up injecting (somewhat ugly) flag links into the mobile view for any comments that you've upvoted. I'll need to fix that, but I thought this would be an interesting observation to mention, even if it's not as practically useful as it might be if more mobile browsers supported user scripts.)
Update: Now that Firefox for Android can run the SOUP extension (as well as other user scripts via Violentmonkey), using a user script to modify the SE interface on mobile devices has become a lot more practical. Accordingly, as of version 1.50, SOUP contains a fix for this issue. Here's what the UI looks like (as of SOUP v1.52):
(Ps. After casting that test flag, I discovered a minor cosmetic bug: the fancy SVG flag icon turns into the word "flag" once the dialog has been submitted. I'll fix that in the next release.)