In general, things that are not strictly digital (PHYs, regulators, PLLs, ADCs) contain significant amounts of foundry IP that would be hard to release as open source. But also, some parts of the chip, for example the AXI bus fabric, were licensed simply as a risk reduction measure. If the bus fabric is bad, you've wasted millions of dollars on a mask set with little recourse. I tried to pull in some open source AXI fabrics and it wasn't pretty...a lot of rework required and even then still some bugs made it through to tape-out. Over time more and more of this can be opened but it all takes time, money, and people willing to do it.
Can I ask how bad it is with lower speed I/O? Less than 20Mbaud, so RS232, RS485, CAN, USB PD/Type-C, 10base-T, ...? The transceivers are rarely integrated, do they need different processes or do they just prefer flexible I/O pins or ...?
Hmm...it's not just the speed. Actually, the I/O pads themselves are closed source because there's a lot of process magic in them - from the ring seals to the ESD protection, the foundries consider these to be part of what makes them different from each other, so they protect those designs.
So for example, many projects bitbang USB full-speed using plain old 3.3V I/Os but by the spec the signals have to have some slew rate limiting in a form that isn't found on standard I/Os. And also, if you're doing it right, you're taking the differential signals in on USB and not just reading them into two separate single-ended pads but you're actually subtracting the analog values to get the full benefit of differential signaling's common mode rejection properties. Thus even a lower speed USB PHY has some specialty circuits in it to achieve these nuances.
As another example, RS232, by the spec, would be a +/-3V to +/-15V driver, which is actually really specialized in the chip world and quite uncommon due to the negative voltages. PHYs that drive I/Os is one of the enduring pain points for open source PDKs - they are hard to develop, "boring" because they are "just wires", but absolutely essential to get right and bring into existence if you want to talk to anything interesting.