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Definitely look at it, totally worth doing or pick yourself up one of the tool head pcbs, I can be heavy handed and having to redo wiring bundles every time I want to change something sucks. Molex connector will work really well if you don't go the PCB route.
As for damaging the board just by running it, the btt boards are super resilient, I've totally whoopsied with my octopus pro and shorted a fan header with multimeter and cut a wire I forgot was live on another. I pulled the jumpers on those headers, rest of the board has 0 issue considering the abuse it had thrown at it. I'd be really surprised if slightly dodgy power would damage 2 unrelated boards in a super specific way and damage nothing else.
This is my thinking as well, but I've got zero other ideas.
I've already cut the wires on my heat cart and thermistors, so swapping those parts around is easy.
I've seen printers with a PCB on the hotend, but I'm not sure I understand what it is that the PCB does; is it simply a port hub between the main board and the hotend to make parts easier to swap out, or does it do any actual "thinking"? If it's the former, I think I've more or less accomplished this with the connectors. If it's that latter, I have no idea how I would go about configuring that to work with the SKR, but it would probably solve my problem by moving the "temp calculation" job off of the main board. It would at least tell me for certain if the board is what's reporting the incorrect temp.
The PCB doesn't do anything other than a compacted connector between components. Especially the surface mount component. Also, some devices can be more sensitive than others making it more prone to breaking during mishandling. If something on the pcb breaks (highly unlikely), then you can just solder using jumper wire (to some degree, high speed signals cannot be treated this way). However, if the component on the PCB is the one that breaks, then you can just replace that component with some careful solder works. But yes, sometimes replacing it will be easier than repairing
I use a version of Hartk's Stealthburner PCB on my voron and cludged an afterburner tool head onto my franken mk3s. They're both breakout PCBs, the stealthburner one to my knowledge is passthrough, afterburner one has a thermistor and led on it for chamber temps and a hotend activity led. Totally optional and what you've done already is probably the more frequent things I'd change anyhow. There are fancier tool head boards, they're effectively their own MCUs afaik that communicate via canbus, with those ones you're running very few wires, something I'm thinking about but haven't done yet
For me, they reduced the amount of wiring I needed to run to the hotend and make it super easy to swap components, as I said, I've damaged things unintentionally before (I'll say ADHD is contributing to that) so it's really handy. Keeps the wiring neater as well, or at least gives you a place to manage them.