vhs-bordercontrol, telecide() and (ml)degrain in vapoursynth

[Selur]

clip.set_output(index=0)
audio.set_output(index=1)

Is probably the problem.
Hybrid will call:

vspipe.exe --info <PATH TO SCRIPT> -

and expects something like:

Width: 640
Height: 480
Frames: 2
FPS: 24/1 (24.000 fps)
Format Name: RGB24
Color Family: RGB
Alpha: No
Sample Type: Integer
Bits: 8
SubSampling W: 0
SubSampling H: 0

output. Since you didn't post a debug output, I suspect that the output for your script looks different and thus Hybrid lacks the frame count and/or the fps and thus does not know the length of the video, everything after that is bound to fail.
As soon as there is an error popup in Hybrid, going further is always wrong.

No Hybrid, was not planned with audio from .vpy.
I'm not looking into audio support for vpy unless there is a waveform filter for Vapoursynth.

but mp4 probably has DAR flags same as prev. mpeg versions....i think one can set them in ffmpeg....

that would be simpler. ie i usually just encode 480x576 and set 4:3 flag in mpeg2 so player corrects it on playback....
(simillar to many weird resolutions of dvb-s mpeg2, for example 544 x 576)

your 640x539 image can't be proper aspect ratio, 640 / 4/3 is 480.

768x576 is correct (attached), in a square pixel world. and preserving vertical resolution.

PAR != DAR. Whether you want to preserve the vertical or horizontal resolution to the original can be configured in Hybrid,...
My screenshot was just to show that 64:45 seems to be the correct input PAR, not that it would create a 4:3 DAR.
Personally, I do not care at all about the DAR unless I need to since I convert to something that only supports a specific DAR. (don't know of any in Hybrid supported format that does)
If you set the correct PAR (correct = no distortion), you can crop however you want without having to worry about PAR&DAR.
If you require a specific DAR, set your width or height and adjust it so that both with in your storage aspect ratio and then letterbox so you got the correct DAR.
This is how Hybrid works. If you don't like it, simply don't use Hybrid.

Cu Selur