Fluff-wise custom built decks are possible, Data Trails has a couple that were not built by Mega Corps. And every project, Mega Corp or Mom and Pop, starts with a proof of concept build or a prototype that is built from scratch. So, it has to be possible. It's just not mechanically spelled out how to do it.
Thus, Houserules would be needed. There was a couple of decent starts in the "How much should a Cyberdeck cost thread?" you could look at.
You'd also want to decide how far back in the process do you want to detail? To use modern day analogies. Are you ordering a motherboard and CPU from Newegg and putting the components together or are you cutting our own PCB boards and laying out the traces? Are you designing your own chips from scratch or are you using off the shelf components?
FYI custom Semiconductors are a thing here in real life, there are foundries that do short run custom work. Expensive as hell though. As in hundreds or thousands of times the costs of mass produced chips. As much as I hate to say "Realistically" a custom built cyberdeck probably is using off the shelf components, like an PSoC or FPGA type of concept where the chips are off the shelf but configured by the builder. And in a world where 3D printers are a thing a custom form factor wouldn't be particularly expensive. More expensive than mass produced, but still in the realm of a few hundred Nuyen. A decent machine shop could crank something out for you in a day or two for about the same cost if you give them the print.
That may have gone a little far into the weeds...
