Your observations about packaging an app for Cloudron are correct, but one you didn't mention is the separation of runtime RO and RW files.
The Dockerfile does seem a little "heavy" but not impossible, and some dependencies added by their apt-get install may already be in Cloudron's base image to simplify it a little.
The biggest issue will likely be the RO vs RW separation, and first look suggests that it might be problematic, needing some workarounds / symlinks to handle where Checkmk expects/needs things.
TBH, one never knows fully with an app like Checkmk until the packaging process is started, flushing out what doesn't work and how it can be handle.
A more professional packager might have a different view - that's just my (amateur) 2p.
