No. Beelining has nothing to do with it.
When buildings replace each other, they do so before the one being replaced is obsoleted in case you just never got around to building it for a while. This wasn't an accident. The accident was that the replacement is worse than the original.
And THIS is a RAMPANT problem in the Modern Era. This is only one of some 50 buildings that have this issue. And the reason for the problem is always the same, the tech bonuses were not taken into account.
Personally, I feel the tech bonuses are too strong. I also feel that the progressions should be charted out to ramp things up with much more care.
But making one not replace the other is returning to the issue of the original building being obsoleted at some point and when it does get obsoleted your civ loses it in every city and takes a significant hit, making the tech a bad thing to get. The point of replacement is to eliminate this sensation and allowing for a smoother transition.
Furthermore, as I stated before, allowing both to be concurrently operating in your cities leads to an even greater glut of research and we're already needing to tone it down a bit. It's the # of sources for research * the potency of those sources that is a bit problematic. If we tone down the amount of research each of those sources gives a bit, we will introduce improvements in balance.
Not that this is the only problematic commerce and/or yield. I think they all ramp up a bit too high, too fast and should really be toned down across the board but do so with a charted and better measured sense of progression.
I think Hydro, Pepper, and Azure, would all admit that they were setting up initial values that would eventually have to be rebalanced and tweaked before we'd have a solid sense of game balance in these later eras.