Both of these solutions require modding your game.
There is unfortunately no good solution achieveable without mods.
Gets around the problem by simply making the lowest-tier / "default" mod for that slot free to craft. Install the "no profit" version to make the standard mod crates (unattached loose items) have zero market value, to preserve balance.
For convenience with Free Downgrades; stops the now-worthless standard mod crates from being created in your inventory when replaced.
This adds a new "weapon blueprint" item and allows weapons to be in a non-functioning state if they're missing a receiver. Seems to introduce a few more finicky items & mechanics than it needs to (it includes a portable weapon mod switching, but not crafting, workstation to swap mods in the field), but makes a little more in-world sense and is more potentially more robust to other weapon mods than Free Downgrades.