Any system beyond a vanilla install will need some tweaks to fit your use case(s). And these tweaks often end up as a stack of glass boxes over time, unless meticulously planned purpose built from the beginning.

As long as it’s manageable and secure, don’t let “perfect” be the enemy of “operational”.

Wanting to rebuild from scratch is pretty common. The question is whether you need to and should. You have to weigh cost and work hours up against any benefits to figure out the answer.