Since it is working now, then it was correct. And yes, it is safe.
Frankly, I wish the option/feature didn't even exist.
Many MANY years ago, there was a marketing push for "multi-rail" PSUs. The [so-called] theory behind it was to created a sort of "pseudo" dual PSU setup with the idea being, should there be a failure on one rail, it would be isolated to that one rail and thus, insure no damage to the components connected to the other rail. It also "supposedly" would prevent one power hungry device (GPU for example) hogging all the power from another device (like the CPU).
It was based on the real-world practice of using multiple PSUs for mission critical systems. In the event one PSU failed, the redundant supply kept the system running, and ensures every device got the power it needed.
But that redundancy capability is impossible to achieve when the single PSU has just one AC input and a single input transformer and a single set of filter caps for that one transformer. So this marketing "push" turned out to be nothing more than pure marketing "
hogwash!" The ONLY way to truly get such protection and redundancy is to use two separate PSUs.
The problem with this feature to split one big rail into multiple rails is exactly what you encountered - the full capacity/capability of the PSU cannot be accessed on any one of the rails because some power is always delegated to each rail - even if nothing is connected to the other rails!
On top of the that, the better PSUs (even back then) are (and were then) pretty smart by design (and, in fact, in most cases, by national and international safety regulations and codes). If they sense a potentially dangerous situation (internally or with a connected device), the entire PSU shuts down output to prevent any collateral damage to the computer components - or prevent catching fire, burning down the house, and ruining the user's day!
Lesson learned is with a properly sized PSU, a single rail system will easily support all the components AND ensure each has the power it needs when it is needed.
Note too, designing and manufacturing a multi-rail PSU cost more. The design is more complex and it requires more parts and thus costs more to build. Then because it has more parts, there are more potential points of failure.
Sadly some companies still market multi-rail PSUs. But make no mistake, it is a marketing "gimmick" designed to earn the company more profit. There is NO technical advantage to using multiple rails in a computer UNLESS the rails are totally isolated by using two PSUs. And even then, the advantage is limited. If a system is
that critical, use mirrored computers.