Thank you for your quick response! I was away for some time so, sorry for my late one. ;-)
The thing is: as soon as I start IndigoStack I get this error and the app closes again. So rebuilding the System stack is not possible. I did try to remove the app and reinstall it. (https://indigostack.app/docs/how-to/uninstall/). In this process I did not remove any certificates, since the one I generated myself some time ago
The reinstall did not magically make the mkcert appear. The helper installs, the error pops up and the app stops as soon as I OK the error..
After the new installation there is no /usr/local/indigo folder and the ~/.indigo/stacks/system-stack folder contains no "mkcert" folder at all.
What I did now is: making a symlink from mkcert in my /usr/local/bin to ~/.indigo/stacks/system-stack/mkcert/bin ..
This did something good, the "mkcert" error is gone. So maybe the existence of the /usr/local/bin/mkcert was an issue?
Only now I get the same error for dnsmasq:
The following error occurred during Indigo's startup: The file "dnsmasq" doesn't exist.
I tried to reinstall my dnsmasq via brew, stop the service and symlink it too, but that does not seem to work.