Short answer: No.
Even a copy to Named Clipboard goes through the System Clipboard.
Although I generally prefer to then set a KM Variable to the CB, there are many KM Actions that work directly on the CB.
If you don't want your Clipboard or KM Clipboard History cluttered with these copies, then you can just add a Delete Past Clipboard action, with a 0 for the Past CB.
Have you checked out the excellent macro system MACRO: [KMFAM] Favorite Actions and Macros by @DanThomas?
It is basically like a template system for KM. So you could store the 3 Actions to copy, set var to CB, delete past DB, and instantly paste them into any macro very easily.
You could even put them in a Group Action so that you could close the Group to eliminate clutter.
Finally, I'd suggest as a best practice that you try to avoid really long macros, scripts, etc. Try to modularize functional elements for reusability. For KM Macros, you would create what I call "Sub-Macros", which are just normal macros called by an Execute a Macro action.
BTW, but KM Instance Variables are designed to work well with sub-macros while avoiding data conflicts with other macros.
Good luck!