Yes
Thank you. It worked really well.

During all the testes I've done I figured that --custom when used with --variable-width-glyphs it messes with the bearings but when --variable-width-glyphs is used with the internal glyphs option of font-patcher it doesn't cause this issue!
So,
-c --variable-width-glyphs everything all right!
-c --custom --variable-width-glyphs messes with the bearings!

Why is that? Is there any plan for it to get fixed in future?

I guess I do not really understand all your problems, but then probably I would need your xxxt.ttf to really examine it, and some example invocations that went well or not well; so that I could really reproduce the issues.

In principle --custom is not a core feature of the patcher and the support is rather ... limited. I used it once for a project (https://github.com/adam7/delugia-code) but that has a specifically hand-crafted custom font.

If I could understand the problem it can for sure be fixed. Not sure if that (fixing) is needed, noone ever complained so either it is ok or it's never used ;-)

The font is Segoe Fluent Icons by Microsoft.
I installed it from AUR through a package.(V1.22)
The one in Microsoft website is v1.0
I thought maybe it's not okay to share it! (License stuff; I don't know much)
But here we go
ttf.zip
If it's not okay, please do tell me to remove it or if it's possible do so yourself.
Thanks.

As per their license we/you can not put it up here, neither modified or unmodified:

You may use the Segoe and icon fonts, or glyphs included in this file (“Software”) solely to design, develop and test your programs that run on a Microsoft Platform, a Microsoft Platform includes but is not limited to any hardware or software product or service branded by trademark, trade dress, copyright or some other recognized means, as a product or service of Microsoft. This license does not grant you the right to distribute or sublicense all or part of the Software to any third party. By using the Software, you agree to these terms. If you do not agree to these terms, do not use the Software.

emphasis mine