My Sonus Faber Amatis have weak bass even though I'm running ML 536s--800 w/ch into 4 ohms

I have Sonus Faber Cremona Ms. I also have two KEF R400B subs to enhance the bass. My amp is a Macintosh MA8950. I know my room has some issues, but I'm ok with using the subs. Sometimes, I turn them off for specific listening, but most of the time they're on. I don't see it as a problem, more of a solution. 

As  mentioned - If new, the woofer suspension will loosen up over time and start to sound as designed, but can sound restricted early on.

Double check that the polarity of the speaker wires is correct at both ends....you can even take a battery with two leads soldered on each end to check the woofers are wired correctly internally. The positive lead to positive input (plus neg to neg) should cause the woofer to surge forward...otherwise they're wired in reverse.

Bass output is relative to the volume it has to fill.  Your room is large with a large volume of space to fill.  It's possible that your room has some bass issues, and the main woofers aren't up to filling it with low frequency.  Subs can be a good, simple solution.  My speakers had plenty of bass at our old house, but I needed a sub to fill the space of our current room.

Do you have any bass controls you can turn up?  You could also try bi-amping to the woofers with a separate amp that has an independent volume control, but both of these solutions could have some complications and affect on vocals in the 80hz to 200/270hz range in addition to lower bass. 

It's not something I've experimented with, so am only suggesting it as a possible option to consider, but perhaps some sort of parametric EQ with good adjustment options below 100hz could help if other solutions aren't satisfactory to you.

It sure sounds like something is wired out of phase. Try reversing one set of speaker cables. 
 

A friend of mine, let’s call him M, has the SF Amatis and another friend of mine, P,  and I went over there recently for a listening session.

M had been tweaking his speaker placement for a good while and while the speakers completely disappeared, the center of the soundstage felt too low and the music felt flat and not as full as with our speakers (Revel Salons and F328Be speakers, respectively), even supported by dual subs. 

We had no idea why this was the case but we left a bit underwhelmed by the Amatis, not given their price, and it wasn’t for a lack of trying by M to set them up. 

I've found that the biggest contributors to lack of bass is either 1 speaker wired out of phase with the other, or it's a room-suckout where the position of the speakers in the room and the listening position are essentially out of phase with one another.  You might find that moving your seating position forward or backwards in the room, even a foot or so, can have a dramatic effect on bass presentation.  

Your subwoofers might be in a better position to positively affect bass reproduction at your listening position than your mains.

I would turn off the subs and focus on speaker/ room/ listening position setup first.  Once this gets optimized, then you can add in 1 subwoofer, then the 2nd subwoofer.  You'll want a helper to assist so you can stay in the listening position while they move the speakers into the proper position.  There are several resources for this including the books from Paul McGowen and the Sumiko M.A.S.T.E.R.S. setup guide that can make this process easier.

Keep in mind that once you start adding in the subs, their settings may dramatically change from what you have them set to now since they need to work with and augment the bass from your mains, not against them.  Integrating 2 subs can be quite a chore to perfect, however once completed, the entire system will come alive.

I would suggest looking at putting together a REW (Room EQ Wizard) setup and taking lots of measurements.  This can help visualize what's going on in your room and speed up the process.