Even a fully "open" modern platform is usually just way too complex, integrated, and often full of abstraction layers.
With an FPGA, you in theory have that within the FPGA design itself for the most part, but it's still integrated and wrapped away so much that the directly relationship between current and logic, and things like an actual external bus with traces you can probe and hook into, is just not as tangible.
But for normal humans that just want to get involved with hardware and dabble somewhat with software/firmware in the context of vintage computing, taking a detour into fpga-world would be a deep unpleasant rabbit hole unless one was specifically interested in fpga's and there was no other viable option (which in the case of custom ASIC's is admittedly quite possible).
Compared to the nightmarish complex toolchains used for fpga's, digging up some datasheets and working with a DMM, scope, and logic analyzer is a breeze and actually quite pleasurable.
I agree with you, though. If I absolutely wanted physical hardware, I'd get a real one, or an FPGA reimplementation on a general board like MiSTER [1] that'd also let me run other cores, or something like the Ultimate 64 [2] (fit's in a real C64 case). I'd be more inclined to buy one of these "8-bit alternate reality continuity" thing, if something like the (FPGA based) Mega 65 [3] becomes reality.
[1] https://misterfpga.co.uk/
[2] https://retrogamecoders.com/ultimate64-review/
[3] https://mega65.org/