I've been running custom kernels on debian systems for about 7 years without running into any problems
it depends on how you define 'the standard linux way'
are you using make install to install the kernel? (works if you are installing it on the kernel you build it on)
are you using the make system to create a .deb/.rpm file (I don't remember the make command for this, is it make kpkg?)
if you are doing neither, then you have the same problem that you can have an any distro, the modules directory is per kernel version, and if you don't compile all the modules you need you may end up using modules that were compiled from a prior version.
I avoid these problems by not using modules for my production servers. This lets me just worry about installing the kernel file itself on the systems.