Well, the renamed installer still had the antivirus popup but this time it was a warning that the file is new/unknown/may be unstable; the last one was auto-deleted three times before I caught on. So a noticeable improvement there.
I can add 'start-dfterm3' to dfhack.init without any trouble - and with a trivial script, get it to auto-launch with the LNP by treating the script as the dfterm executable. Trying an absolute path just threw errors...
CD "C:\Program Files (x86)\Dfterm3\"
dfterm3.exe
The arrow-key issue turned out to be some odd combination of my light-weight laptop being a little underpowered to be running all three parts at once and having truetype enabled for a while, which makes the menus look awful. I also switched back to the vanilla 16x16 tileset, but that just let me compare more easily.
Unfortunately while the plugins work fine (not that I tested, but no error messages) mousequery is still not working. If I can somehow get this, dfterm3 will be in the next version of my LNP... Edit for clarity: mousequery should be usable locally when not using dfterm; not work over dfterm - that would be a possible problem. It's that the command isn't recognised in this special dfhack edition.
Thanks. I managed to play for a while with my screen folded down, typing in the web interface on my laptop and watching on my phone ^_^ Awesome.