...no easy way to trace where a package of files had been installed...
I guess most of the executables ends in %unixroot%/usr/bin or %unixroot%/usr/sbin as with other *nix systems. Configuration is often placed in %unixroot%/etc but this depends on the application too of course.
Although this means you loose some kind of control over the place where some programs are installed, it's not that bad as it sounds at first. Guess yum/rpm installation will only be used for ported utilities and applications. Hardly anyone will ever pack native OS/2 apps into rpm. So you do not have the usual level of control only for packages you did not have in the past anyway. You do not loose something but you get new ported stuff. And for this kind of apps you have to 'learn' some of the *nix paradigms anyway. Like finding the config which is on *nix usually not in an ini file (os2.ini or some ini in the programs directory or in mptn/etc or....?) but in %unixroot%/etc.
If you want to use parts of both worlds (OS/2 and *nix) then you have to know how to handle both of them. The OS/2 knowledge you gained during the last decades is not enough anymore. Time to learn something new....