Sure, but you're interfacing with it over Jamma, not JVS. The video signal is going over the Jamma edge at 15khz, the native resolution for all these titles. So your tri-sync is in 240p mode basically.
This is mildly off topic but - from what I've seen, on most cabs you can actually send whatever resolution you want through the JAMMA edge as long as the monitor can support it. For example, in my Blast I run 31k VGA video into the JAMMA edge (through a JVS IO that handles sync combining and level matching of course, and with the monitor DIPs set to 31k mode).
The JAMMA wiring just directly passes the RGB + Sync signals to the monitor. JAMMA wiring in and of itself shouldn't introduce additional processing of the signal, so it's up to the monitor to support (or not support) the resolution you send in.
In my opinion it's actually vastly more convenient to send everything through JAMMA, since it makes changing games faster and easier. It also reduces the chance of one possible problem - a lot of monitors that will take both a JAMMA and a VGA input actually have
both inputs connected at the same time at all times, meaning if you accidentally connect both sources at once you can potentially run into issues.
Now as for whether the
MiSTer is sending at 15kHz or not I can't comment - I don't have one (yet). But at least in theory a MiSTer connected to the JAMMA edge
could send 31kHz RGBS, and 31k-capable monitors would be able to display it.