Thanks for the suggestion; I followed the command given by Andrew and it worked:
I read that message, and yes it should work, but I think that on the first update you will make with apt-get or aptitude, the system may say your software is broken. I never tried that command, so I can not be very affirmative about that...
The first time I launched lyx, it found without any problem my texlive installation which is on /opt.... debian installation of texlive (2012, one year late...) is on /usr. Who can understand!
Well, in my opinion, good softwares does not have a lot of hard-coded data (some are mandatory, but in a lot of softwares I know about there are hard-coded things which could be sent in configuration files).
Now, I can see 2 ways to make a software working without any change in the situation you described:
1) you have /opt in your path, and lyx uses the path to find it's stuff2) lyx have hard-coded stuff to locate it's dependencies in various places.
I would tend to bet on the second, since I became pessimistic after having read few source codes of softwares which actually works... ( And, if you wonder why I do think that the 2nd approach is bad: what if the user's system uses a completely different approach for the folder scheme? He will need to change hard-coded things, and recompile. And if he only uses the standard way of his system, the software will make useless checks, while in the 1st way all of that things would be made automatically. Of course, there are drawbacks to automatisms too, like the need of a valid fallback and probably calls to non portable stuff. )
Anyway, it is able to manage that situation, which is definitely a good thing. I guess that tex related stuff have some nice quality standards, maybe because it's not used by average users and so face a lot of different situations.