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Trying to create a temporary alt.ini for my MiSTer for the aforementioned resolution via HDMI. Temporary meaning I cannot use my BVM just now for a few weeks/months. How should I set the vscale etc. in the ini, so that the aspect ration of the cores would be 1:1 and not stretched? I cannot get my head around this 
Aforementioned where?
1:1 aspect ratios are not accurate 99% of the time. The correct aspect ratios of analog video output for each core is going to vary and it's already driven by the analog video output. If you are doing this via HDMI, what kind of BVM with HDMI inputs do you have that has that kind of extreme aspect ratio? That's what is called a super-ultrawide aspect ratio (two 1920x1080 monitors wide, next to each other).
Sorry for being unclear 
I'm using my ultrawide 3840x1080 IPS monitor via HDMI as a temporary solution, because I cannot use my BVM (using VGA out) at the moment. As a default the resolution of the cores is strecthed all over the place... How can I have it with correct aspect ratio in the middle of the 3840x1080 display with black borders on the side? 
Are you sure your monitor has its internal options set-up to respect the original aspect ratio sent to it, and not stretch it?
Fixed! For some strange reason the aspect ratoi setting of the Samsung monitor is in a really weird location in the OSD. Found it just by accident. Thank you AmanoJacu 
I'm glad I could help, I bought a wide 21:9 LG monitor some months ago and the same thing happened to me, the mister was all stretched to the full width, I had to look for the option in its OSD to respect the original ratio of what it receives.