Room/speaker interaction is a challenge at low frequencies. Compared to the relatively minor frequency response differences between two different high quality subwoofer systems, what the room does to wreck their smoothness is huge. That's the main problem, so imo that's where the main focus should be.
In a large live-sound venue, you may at times want to cluster the subs together in front of the stage to avoid having a "power alley" down the center of the room, which would be where widely-separated subs combine in-phase (which would also happen elsewhere but in comb-filter-patterns across the rest of the room).
In a small room, often the opposite approach works well: Multiple smaller subs spread around the room. The end goal is the same: To avoid strong in-phase and out-of-phase regions that result in large peaks and dips. With this approach the subs' outputs are de-correlated relative one another. It's not as efficient from an SPL standpoint, but if smooth bass with good impact and pitch definition is the goal, the slightly reduced net efficiency is worth it.
With a distributed multisub system, each sub naturally generates a unique peak-and-dip pattern at any given location in the room, and the sum of these dissimilar peak-and-dip patterns is far smoother than any one alone. Also the spatial variation in the frequency response (variation from one location to another within the room) is significantly reduced. So if there is still a problem, like your 50 Hz dip, chances are it's a global problem and therefore a very good candidate for equalization.
Given your unusual room situation, it might make sense to distribute subs in the vertical as well as horizontal planes, which can take some creativity. Usually elevating one sub so that it's closer to the ceiling than to the floor will help, but with tall ceilings that much elevation may not be possible.
I have customers who report +/- 3 dB in-room measured response across the bass region (20-80 Hz) from a four-piece multisub system, without EQ. From your post I think some EQ may be needed in your case.
Just as clustering multiple subs in a large room is an acoustic solution to an acoustic problem, so too scattering multiple subs in a small room is an acoustic solution to an acoustic problem.