i do not use Bookerly myself nor have it side loaded. i do know that Bookerly presented some Kobo rendering issues in the past (posts) which appeared to be related to source/font version and possibly epub/kepub type.
Make sure you have the latest available version of Bookerly. Not sure if
this is the absolute latest one but it appears there are 3 font file versions -- one for "display", lcd and other (e-ink?). Not sure whether one should side load the "display" version or the regularly named (other) files -- i assume the lcd font set will be the worst(?).
From the sounds of it.. this is a font file content issue -- not necessarily corruption but due to the rendering parameters the particular set of font files were generated with. (As previously indicated, i have not experienced this with the font i use on my Libra 2 -- the only thing i have noticed with the last 2 firmware releases is some residual ghosting with the "back arrow" from the dictionary page.)