How to specify different flags for inputs with FFMPEG?
Suppose a video stream is 1440x1080 with sample/pixel aspect ratio of 1.333, leading to a display of 1920x1080. Realize that the actual resolution of the stream, and what's stored in the file, is 1440x1080. The aspect ratio flag tells the consuming app (player/editor..) that the intended display proportion is different than the raw ratio of the width to height and that it should use the aspect ratio to rescale the video to produce an accurate display. FFmpeg will not automatically make a video square-pixel since the user may not want that.

The stack filters require that all streams have the same size at the interface that they are joined at - for hstack, that's height, and for vstack, that's width. Only the raw size matters, the aspect ratio is just an informational flag.

So, you'll have to rescale the first input before stacking.

Use

ffmpeg -i vid1.m2t -i vid2.mp4 -filter_complex "[0:v:0]scale=iw*sar:ih,setsar=1[vid1];[vid1][1:v:0]vstack=inputs=2" -map 0:a -crf 24 -ac 1 -c:a aac -b:a 128k -movflags +faststart output.mp4

As far as the encoder is concerned, it is just presented with one stream of 1920x2160 - the historical provenance and composition is lost. Now, if you want to apply different levels of compression to parts of the frame, that's called Region Of Interest encoding. Some initial patches were applied last month to allow this for x264 and x265, but it is not operational yet. I'll update this answer when it becomes so, but for now, you can only assign a single CRF value for the whole frame.