Fair, but it's just a tooling issue. You don't debug your Verilog anymore at the gate-level, do you?
Also, "just a tooling issue" is a pretty big problem when you're talking about something that wants to be adopted as part of the toolchain.
The word "just" is carrying the weight of the world on its shoulders…
FPGA toolchains are infamous for one of the worst and cursed toolchains in the world. Where writing tcl scripts to imperatively connects blocks together in a block diagram that will integrate all the verilog code is not just normal, but encouraged. Because their internal block diagram description file is git hostile