My belief is that the client or GC or both missed the mark to what the desired end result would or could be.
IE it's not your problem to fix.
The biggest problem I see is that notching wood to install anything in any fashion will involve getting the
structural engineer involved for blessing and sealed sign-off.
Sure the linked pages show illumination spread for various designed layouts, you don't or didn't get that nor have the luxury.
Point is IMO you didn't have enough distance with the angle of the roof and the top of the center beam to illuminate correctly.
The real problem in this situation is that the quality of the illumination can't be de-picked correctly in CAD. It's an angled roof.
LED manufactures use Kelvin to show light "warmth" or hues of color but have generally all but abandoned spread patterns.
This spread is implied with pretty illustrations but not detailed for the end user to install.
Here what I'd do, if your still involved.
If you get the sign off on making holes. In the rafters, set up three different types of very good LED strips.
Center one on beam, a bay over, set up a pair sided by side on center of beam, third bay install a piece of 90* aluminum and place
a strip on each side. Let the owner see them illuminated into the evening-night. They probable want them to dim-able so keep
that in mind.
I believe I'd put everything on an aluminum strips to help with heat build up.
Good luck