Hi!
If you use the scan you already got as reference in e.g. fusion360, you can rebuild this piece in matter of minutes and it will give you better result (surface quality) for sure. Highly recommended to do it like that.
You are right, it is all about right angle. If there is a “shadow” from one angle, infrared scanners won’t be able to scan that area (as exolained e.g. here by @PUTV Capturing nooks & crannies in bones - #2 by PUTV ).
But I see you already scanned the walls of the holes. On such narrow holes scanning from bit farther away should enable the cameras to see deeper into holes. Maybe some matting spray (foot spray or dry shampoo spray) can make it easier to scan already hard to see areas.