Thank you Aditya,

> My question is then how
> do you usually run mtxrun:
> 1) always writing the full path of the correct executable,
> 2) avoid putting [lmtx path]/bin in PATH,
> 3) putting [lmtx path]/bin _after_ [lmtx path]/tex/texmf-linux-64/bin in
> the PATH
>

I always follow 2. I don't think that [lmtx path]/bin should ever be in
the PATH except when updating the installation.

Then I will go with option 2), and report back if I encounter any problem. If this works well, then it could be useful to change the message shown at the end of the installation process, as Rudolf already suggested in this thread.

By the way, you seem to imply that [lmtx path]/bin should be in the PATH during updates. I didn't know that and I'm sure I've updated several times without it: I have different environments to be able to switch between different versions of context (lmtx, the old one, that from texlive...), I never check which one I'm in before updating lmtx and the installer does not complain. 
 
LD