It's a leaky abstraction over the underlying system call mechanism. Because the user stack lives in user space and accessing it from the kernel requires the same dance as any other access to user memory, system call arguments are instead passed in registers where they are immediately available to the kernel with no possibility of faults or TOCTTOU holes.
Here 'unsigned long' is just a convenient stand-in for "generic register-sized argument".
A "void * pointing to struct" requires a copy from user space. If a particular prctl() does need a struct, it can certainly stuff a pointer into one of those 'unsigned long' parameters (in the kernel environment, a pointer can be converted to and from an unsigned long without concern).
On all Linux architectures, "unsigned long" and "long" are always register-sized. For 32-bit architectures, "long" is 32 bits (the same as "int" which is always 32 bits), and for 64-bit architectures, "long" is 64 bits (the same as "long long" which is always 64 bits). This is different from Windows, in which "long" is always 32 bits, even on 64-bit architectures (and you have to use "long long" if you want 64 bits).
Therefore, Linux-only code (including the Linux kernel itself) commonly uses "long" or "unsigned long" to mean "register-sized" and "large enough to fit a pointer"; portable code normally uses "size_t" or "uintptr_t" for that.
It's not even just Linux - way back in the mid 90s there was an agreement among UNIX vendors to use the "LP64" model for 64 bit architectures, and ILP32 was already the de facto standard for 32 bit UNIX-likes, so "long can hold a pointer" is somewhat of a tradition in the POSIXy world.
Because this is the most general signature possible (in general syscalls can have up to 6 arguments because the kernel supports x86-32 which has only 8 general purpose registers of which one stores the syscall number, one the stack pointer which cannot be reused due to signals in case of no sigaltstack, and the remaining 6 are available).
Depending on option, the args can be pointers to structure.
prctl is responsible for setting certain privileged CPU registers on certain platforms. I can imagine some benefit of having the values already loaded into registers for such a brief call instead of having to go out to user-controlled memory (which needs to be accessed carefully within the kernel).
It’s also worth noting that most older Linux system calls do not follow that pattern in general, so I don’t know that I would consider void* idiomatic for system calls until recently.
Here 'unsigned long' is just a convenient stand-in for "generic register-sized argument".
A "void * pointing to struct" requires a copy from user space. If a particular prctl() does need a struct, it can certainly stuff a pointer into one of those 'unsigned long' parameters (in the kernel environment, a pointer can be converted to and from an unsigned long without concern).