This sounds like a hobbyist project which is fine but if so, why so worried about data cost?
Concerns about data
1kB/hr ~= 0.72MB/month = $0.29/month in data. Even if particle / mkr with their built-in libraries use 3x that, then that will cost you $0.86/month in data. Very cheap compared to the cost of any of the boards you are looking at. I think focusing on data costs really only makes sense when you have many units (1000+) or if you truly need realtime data transmission meaning you are sending lots of small messages (like multiple messages a minute).
If you are looking to do high volume then your best option is to design your own board where you can use any MCU / modem / power supply / etc.
Capabilities of MKR1400
Note the mkr 1400 doesnt have dedicated EEProm but you can use the flash memory as non-volatile storage (see http://forum.arduino.cc/index.php?topic=561182.0) This is common for many microcontrollers (see the whole Espressif line of WiFi MCU’s) and is better in many ways as you have access to a huge bank of non volatile storage instead of a few bytes with dedicated EEProm. Note the U201 modem can also store data in its non volatile memory with a few AT commands.
The SAMD21 chip on this board also does have a deep sleep (I think they call it Standby) that will draw in the few 100’s of uA. See this video: http://forcetronic.blogspot.com/2016/09/reducing-power-consumption-on-arduino_24.html Anything on the Arduino Zero and sleeping will also apply to the MKR boards, its the same MCU.
Handshaking on different boards
The bandwidth used on each board really depends on what cloud system they are connecting to. You can connect to Hologram’s cloud (or your own) with Particle, PyCom, MKR or other boards. This may require a bit more programming but really you should just be able to follow along the Dash’s code and copy-paste most of it. Its likely Particle’s cloud uses HTTP or some protocol with more overhead than Holograms embedded API so their examples show higher overhead (as I said above, I woudlnt worry too much about it in your case anyway).
Pi, Nova, Tpl5111
Wow that would be a real mess of a system and definitely not low power, that would involve booting up a linux machine that draws atleast 100mA just to to send a small message. Remember overall power consumption = [time in standby] * [standby power] + [time active] * [active power]. Your [time active] would be much higher with a nova and likely be worse than just leaving a mkr 1400 active the whole time.
The MKR 1400 really can do everything the Dash can do, it is your best option. A Pi with a Nova and a timed power switch is definitely not a good option for many reasons.