The all Mastervolt solution looks good if you enough $$$s.
Regarding your questions, here's my two-penny worth
1. Bowthruster : It's 99.99% sure that you will have the main engine running when you are using the bow thruster. The engine alternator will be charging the house batteries. The bow thruster doesn't care what kind of batteries are powering it aslong as the voltage is correct and the battery bank can supply enough current. That won;t be an issue with a big bank of LiFePO4 batteries, just as it's not an issue with lead-acid batteries
BTW I never heard of anyone running the genset when using the bowthruster.
2. Starter battery : This is a completely separate system from your house bank. For a start (pun intended) the start battery is 12V and is charged by the small; alternators on both the main engine and the genset. This battery can be any kind of 12V battery you like but for max CCA you should use lead-acid.
3. Solar panels are great, most efficient if you wire them in series and use an MPPT controller to regulate the voltage. Mastervolt have one that has a profile for LiFePO4 batteries.
4. Capacity : you need to work out your likely consumption ..Bill / ex Bebe published a spreadsheet here with consumption figures that will approximate yours - you can go through it and change for 53 - 54 differences.
Then ensuring that you don't exceed the DOD of 80% and adding a buffer, you can calculate your needed capacity.
I'm sure will all be very interested to hear how it all works out.
And just a niggle from me, I wish Mastervolt would not call these batteries Lithium Ion when they are Lithium Iron Phosphate batteries.
Lithium Ion batteries use lithium cobalt dioxide or lithium manganese oxide as a cathode.
LiFePO4 batteries use lithium iron phosphate as the cathode material.
These batteries have quite different characteristics.