I've been playing through the Gold Box games, EOB, and M&M which all have handy 3rd party automapping apps (Gold-Box Companion, All Seeing Eye, Where Are We?) but the problem is I like to use other builds of DosBox like DosBox-X and DosBox Staging or SVN builds but none of these apps seem to work with those. Has anyone figured out how to point those apps to a running instance of an alternate DosBox build?

For this topic I'm talking specifically Where Are We? which I'm using to play M&M1.

You can try disabling options such as "DOSBox memory quick-scan only" and "warn if process is re-acquired," but there's only so much leeway to be found. I've had luck running it with DOSBox 0.7.4, but other branches are probably out of the question without an update to WAW itself.