Have you done any listening to any of the prospective pieces of gear you've listed?

A laminated floor and floor to ceiling windows will make getting decent sound very difficult.

Audition some speakers and gear and let us know what you think of what you hear.

I'm fairly certain almost any one who posts here will suggest you actually listen to some gear, especially speakers before you make any kind of decision. 

Some nice thick ones.  Depending on your tastes, that may be the most important component in your system.

I have indeed. Both speakers connected to a Marantz PM6004 and a Roksan K2 in a proper listening room of a good Hi Fi store, and the RX6 were definetely better and more enjoyable given the right room setting.

The question is, given that I can't transform my room - I can do some improvements like area rugs - but not transform it; would the RX6 be "too much" and ultimately counterproductive?

Any views? - Thanks    

transform the SIZE of your room but you CAN transform your room to make it more friendly to larger speakers.  Area rugs, heavy curtains along the glass wall with all the windows.  And you're probably helped by the length of the room, assuming you're running the system into the length of the room and pulling the speakers out off the wall a little.  You're limited by the low ceilings, but I wouldn't let that keep you from focusing on the room before you start really laying out scrill for the system.

Thanks to all for your advice. The message is clear, first step is to improve acoustics of the room and I'm alredy working on it.

So the remaining question is, assuming improved accoustics in the room, what system would you go for?, - my options are:

1. MA BX5’s / Marantz PM 6004 / Arcam rDAC / Sonos connect – Total cost c.a. $2100
2. MA RX6’s / Arcam FMJ18 or Creek Evolution 2 / Arcam rDAC / Sonos connect – Total cost c.a $3400

I'm really interested in your views. Thanks.

I'd also at a minimum budget for bass traps for the four corners and mid/high absorption for the first reflection points at the side walls and ceiling. 

Something like GIK TriTraps or 244s in the four corners and GIK 242s at the first reflection points. Then, if you can, look at GIK 244s for the front and back walls. 

There are other similar products available, but the idea is the same for basic treatment to tame a room.

http://gikacoustics.com/products.html

http://www.atsacoustics.com/

http://www.realtraps.com/index.htm

Of your proposed systems, I really like the Monitor Audio RX6s, which could also be mated with the Marantz PM 6004 / Arcam rDAC / Sonos connect for a satisfactory system. As long as you like how it sounds, should be great. Good luck!