It is discouraged to use apt to update the system in KDE Neon, One should use Discover or the command: sudo pkcon refresh && sudo pkcon update to update the system...

My question is, besides updating the system(sudo pkcon refresh && sudo pkcon update) Is it ok to use apt/apt-x/dpkg for everything else ?

For instance, Under Kubuntu, I do the following:

(1) To remove older kernels and other residues I use: sudo apt autoremove --purge

(2) To clean out the cache I use: sudo apt clean

Yes.