I realized that Aegisub misloads subtitles included in MKS with subtitles only.
In short, of each anime series I am making a backup of the subtitles but inside an MKS (this is because MKS also allows you to keep attachments / fonts together and makes my life easier if I have to put them on other video tracks, ex: BD).

I can guarantee that the problem (from a simple point of view) is Aegisub's:

1. SubtitleEdit opens subtitles without problems (and also loads the fonts even if they are not installed on the PC);
2. If I extract the subtitle from the MKS and open it with Aegisub, there is no problem;
3. If I mux the MKS on the video track, the subtitles start with the right timing (if it is the same track of course).

Luckily I noticed this, I don't know how many blasphemies ... if it was a bug of MKVToolNix.

I add that even in some cases it also moves the lines (some lines such as comments are placed at the top of the script)

Thank you in advance.

Here are two examples and files to try using:

MKS: https://mega.nz/file/1tF3XKjQ#lx8Eaa47SvChy6QuMphRyJxoGti3mjj7MyEaX3btteI
ASS: https://mega.nz/file/ZhUVkCgI#d5Kk64w1oSgPM8ssGyboX2qq2n1Qj1N1NfkcO-U0574
Video Source: https://nyaa.si/view/1304005

Original file with the right times:

MKS opened by Aegisub (wrong times):