I've always wondered why that is. Isn't the ride designed to handle that? Asking for a freind because I'm not sure.
As I understand it this is the biggest reason. Nessie is old and they avoid it to prolong her life. It creates a lot of stress and force when both trains go through the loops fully loaded at the same time.Metal fatigue and/or loss of ground compaction due to excessive repeat vibrations from operation - something Arrow didn't originally accommodate for in their design since they way overbuilt the ride and figured it'd be fine.
That, and they probably didn't realize what 40 years of operation would actually be like... Just my guess as to why they're intentionally running without the trains going through the same physical area at the same time.