It says 60FPS in each case (or does it jump up to 60 when you pause?).
And, yes, it will definitely depend on real wall clock time. The CMOS clock chip is emulated simply as a pass-through to standard C library system time calls. If the game is running at 60 FPS, it should be fine, unless it is doing its timing one frame at a time rather than one second at a time (e.g., MHz = cycles / T where T is measured as milliseconds from beginning to end of frame, which will be less than 16.67 ms on a fast computer).
By the way, look at line 29 of RTC72421.cpp

That comment has been in there since day 1.
I actually think the emulation should remain this way although we could add a mode that computes time from PowerPC clock ticks.