If we can agree that more starbases are good, the question is only whether the price tag of ignoring the cap is worth it, and in which cases.
I think you have the right approach but draw the wrong conclusions.
Yes, a cost-benefit analysis is important, but it's not sufficient- it doesn't follow that you should always go above your starbase cap if building a new station will bring more income than it costs. You also have to make a cost-minimization analysis: How can I achieve what I'm trying to do most efficiently? And the answer is, as people have pointed out before me in the thread, rarely to go above starbase cap. Optimizing your starbase layout (for trade collection and piracy protection) and getting rid of redundant stations is almost always better than just going above cap when you really need to keep a newly acquired base to collect trade from your recent conquest or whatever (this is the most common situation I find that I have to make hard choices about which bases to keep and which to downgrade). When it comes to naval cap there are also alternatives that you have to consider, and if that analysis doesn't include a consideration of taking an ascension perk you're not taking the problem seriously.
Going above starbase cap for trade collection is bad mojo. The reason for that is that unlike the simple analysis on the first page, the actual cost of expanding your empire's trade network isn't just the upkeep cost from the new hub and going above cap, but the piracy effects that cascade downstream and require even
more starbases to counter. It's still possible that it's the right choice in some situations, particularly in the case of piracy suppression (if you're generating enough trade to have starbase cap issues, adding a star fortress full of hangar bays is often a lot more impactful than adding another trade collection base) but it should be a sign that you've misplayed somewhere and you're taking efficiency losses as a result.
That leaves anchorage bases, and yes I can agree that in some cases (eg gearing up for a war scenario where you need to build above your regular naval cap) it makes sense to expand beyond the starbase cap to increase your naval cap. It's still contingent on not having better alternatives (galactic force projection, naval cap tech, strongholds and certain edicts come to mind) but it's not inconceivable.
In the final analysis, though, you want to a) avoid going above starbase cap if you can, and b) try not to stay above cap any longer than you have to.