Of course the factory rep would say there are no problems...
When the cylinder temps are not even and there is no main bearing I'd say there is a fundamental design issue.
Does the engine run? yes
Could it be better? yes
Is there anything to gain from the modifications? yes
Should the engine have been designed and manufactured like the mods suggest? yes
Why?
1) Even cylinder temps = efficiency and performance
2) Main bearing = more RPM - reliably
3) Cost impact to production = minimal if not cheaper due to less aluminum used and simplified intake plentum means less machining time plus addition of SAE brass bushing.
4) bottom line = more performance than the stock engine with mods that should be standard production spec.
Unfortunately this the only engine in this class so you have to make the decision to buy it, stock or mod it.