following scenario: two adjacent factories, sharing in/output.
Pick them up and try to put them anywhere else.
You can't place the second factory as the relays are blocked.

Current workaround: remove the relays, place the second factory and re-create the relays.

Is there any chance to avoid this and allow to place factories adjacent in case their relays match in position and type?

A simple workaround: Place something to block the relays of the first factory, like an assembler. Place the first factory, and because it's relays are blocked you can break the assembler and put the second factory down. They will automatically link when you do that.

It's not ideal, but there's no easy way to code it without things being even more confusing unfortunately, the Factorio API just isn't flexible enough for weird situations like this.

Yes, your workaround is better as it avoids re-creating the relays, thus losing the resources inside... I understand the code-related trouble, so it's fine. Thanks for your fast response.