It's not too difficult to fix the alignment of the glyphs. These are individually set in the LevelUpMenu.swf file, which is packaged into the Interface archive (Fallout4 - Interface.ba2). If you did this you'd want to provide it as a loose file or as a re-packaged archive. The tools you'd need are BAE to extract the original from the vanilla archive, then JPEXS Free Flash Decompiler to actually locate, modify, and save the values. I could provide more detailed instructions if you were interested in doing this.
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