Many applications perform runtime checks and alter their behavior accordingly. One method people use it to check if the SNAP variable is in the environment; you could use this to conditionally prepend /var/lib/snapd/hostfs to the files which could in theory be abstracted to a single helper function which wouldn’t require separate code bases and shouldn’t introduce problems.
I’m still of the opinion that this fits broadly into the supported ‘IDE’ category and open to granting classic, but considering the above and that great care must be taken for classic snaps to work reliably across all distributions (see ‘Caveats’ from Process for reviewing classic confinement snaps), are you sure your application can’t be made to work well in strict mode?