There’re tools like KiKit to do penalization. If your work is simple, they work fine. If your work is complex, they usually work, in a complex way, maybe with some codes. If you want to burn/test all boards with a single group of pinheads and catch mistakes with DRC. It seems no tools can help. But with a very small change, we can do all these in KiCAD itself.
Here is the idea: We already have “Paste Special” command. And we already have the option: Assign unique reference designators to pasted symbols. All we need is a new option: Append a postfix to designators of pasted symbols/nets. Now you can put them anywhere you want! Then we create some mosebites connections in footprint libraries. Now you can do any kind of penalization, all in KiCAD.
We can do the same thing in schematic, so every part can be different.
I would not use that old 2017 topic for advice though. Development on that panelizer seems to have ceased. There are better alternatives now. The adavantage of that panelizer written in C# is that it works at the Gerber level so not specific to any ECAD suite.