This doesn't apply to games that use vsync.
That's completely transparent to the viewer if they don't read the commentary text; it shouldn't affect their enjoyment of the actual run.
Downgrade the encoder and/or MKVToolNix, or try it without the batch file - for example VirtualDub + x264vfw, or a manual call to x264 with only the most important parameters (e.g. "--crf 16").
AvsPmod is just an Avisynth text editor with built-in preview.
You could try specifying the framerate in MKVToolNix; this would only work if all frames have the same duration. Otherwise it might work with timestamp files (though I wouldn't know how to generate them from a source file).
240p
The SNES is a bit difficult because it does the progressive trick (i.e. leave out the last line and make the total number of lines per frame even) and varies the number of clock cycles per line.
The mainboard clock is 5*7*9/88 * 6 * 1,000,000 Hz. There are 1364 cycles per line, except for line 240 of the second field in progressive mode which has 1360 cycles. That results in (1364*524 - 4) / 2 cycles per field, and a field rate of ~60.0988 Hz. Meanwhile the capture cards expect the standard field rate of 60/1.001 = ~59.94 Hz, which is why they might show a "skip" every few seconds.
So they can't render at 60Hz at all...
Easily recognizable because of the scanlines.
A full NTSC frame (including overscan/blanking) is 525 lines, 262.5 lines per field. The first (upper) field shows 262 full lines, and the last one ends up in the middle of the lower border of the CRT. When the electron beam jumps back to the top, it continues in the middle, drawing the new lines between the lines of the previous field.
The odd number is what causes the interlacing. Consoles with progressive mode just omit the last line, which is why those modes are also a little bit faster (1/525 = ~0.19%).
Yes. There are for example very few SNES games that use interlacing, mostly just for static screens. RPM Racing is the only one that uses it in actual gameplay, afaik.
LUA doesn't have a "count_sprites_on_screen_in_SMS_Lemmings" function. That's very game-specific.
Either use the cheat search function to find values that decrease when sprites disappear and increase when new ones appear, or... you'd probably need to disassemble (parts of) the game code.