Just a random thought.

AFAICS the path translating in compatibility mode is
here in big part to ensure the linux/whatever program reaches the right
shared object. 

What if we would have our own /lib/ld.so
with specially hacked dlopen(), so that it would open
/emul/$compat$file if it would exist, instead of $file.
Otherwise there would be no additional
path grokking. Would it be enough ? The /usr/lib/ld.so
could even be just a wrapper, which would replace itself
with something like a /usr/emul/ld.so.$compat. 
There could be even handful of some other necesary linux tools
(linux-ldconfig comes to mind -- it can't use "native"
/etc/ld.so.conf).

Is it totally stupid idea ?

There might be problems for files which have same name
name under Linux and NetBSD, but have other format.
I can't see if this is really a show stopper.

-- 
Jaromir Dolecek <dolecek@ics.muni.cz>      http://www.ics.muni.cz/~dolecek/
"The only way how to get rid temptation is to yield to it." -- Oscar Wilde