I am currently rebuilding a Yam 1974 DT250 engine, it also has these 3 holes filled with some epoxy around one of the main bearings.
I think I remember my Suzuki RL250 engine having the same thing as well , I guess they are used maybe in the manufacturing process and then filled in after ?
I heated the cases up on the RL250 engine and changed the main bearings without any problems regarding these holes.
I am sure its not a problem, if the epoxy isn't loose or anything .
I expect someone on here knows their exact purpose
hope this is helpful