Short answer is: No PAL games have different lag and various methods to compensate for said lag, so running it in a faster speed is by no means equal. The fact that you don't even reach the same FPS should just further hint that it's not a valid thing to do.
the system is pretty identical as far as I know, the PCB just literally has 3 points for PAL/US/JP positions. A lot of games run the 1:1 code on each mode, some games have custom routines to compensate for the slower execution speed in PAL mode and some just swap the title screen and other localization stuff around. I have been playing games on NTSC 60Hz mode with my MD and it seems to match the NTSC spec just fine. MD doesn't need any custom crystals or such, it just shorts different pins. Unlike nintendo, MD/GEN recycle the hardware and the games.
I can double check what it more precisely outputs.
A) No region lock, unoptimised PAL 50hz games. Basically the games will change region, based on the switch (EU/US to JP) and matches the 60hz speed when switching the console to 60hz. Examples: Streets of Rage and Revenge of Shinobi
B) Region locked, optimised PAL 50hz games. Restricted to certain regions and setting the game to 60hz will perform much worse to a PAL copy than optimised 50hz. Examples: Sonic 2, Sonic 3 & Knuckles
C) No change, basically not noticeable when changing the hz switch to me at least. This needs more research. Examples: Corporation (Cybercop in US)
D) Region locked, unoptimised in 50hz. Very similar to example A but basically it's region locked to a NTSC-U or NTSC-J region. Examples: Playing Bare Knuckle 3 (NTSC-J), Castlevania Bloodlines (NTSC-U) on a unmodded PAL Megadrive by using Region converter carts.
Still in a lot of cases, the ROM data is still identical. There is just a different branch in the code depending on the region you have. Sonic2 for instance will check this at the boot, switching in mid game can cause issues (sonic1 actually starts stuttering when you go from 50Hz to 60Hz without a fresh boot even though it's not speed "optimized")
So in many cases, as long as you boot with 60Hz and US/JP, you will get the same result as with a native US/JP console
Searching for goodset dumps can be a good starter to see what games share the same ROM globally (labelled JUE usually)
Generally if you boot up in NTSC mode and the game doesn't give you a 'wrong region' warning, you should be fine. Hardware is the exact same except for the pins being connected differently (as said before). It's possible that your framecounter doesn't count still frames if you're getting something slightly below 60.