House battery bank 1 consists of 4 6 Volts batteries connected in series
And the bank 2 has two 4D 12volts bats connected in parallel
I.E. 24Volt house bank, presumably high A/H capacity, and 12V start bank, also high A/H capacity...
My question is 1) is there any advantage to this choice of bats
Conceivably; you can reconfigure either bank to be a back up for the other. That's a good thing... But I am guessing that you have a vastly over-provisioned starter bank. If you don't need all those A/H for your starter (and I'll bet you don't) you could probably do away with one of the 12V batteries, and still survive any single
2) is it preferable to have two identical battery banks
No, the two banks serve two different purposes.
Like two sets of 4 six volt batteries
Istead of two different banks
You could probably get a quantity discount when buying batteries.
3) having two different banks would that in anyway adversely affect the
Performance of my xantrex MS 3000
Also my starter bats are also connected to the charging system. Is this advisable.
My boat electrician installed a combiner with the wirings.
I'm gonna go out on a limb here and guess that your "boat electrician" has a better handle on your electrical system than you do.
I respectfully suggest that you buy a book that covers sailboat electrical systems, and read and comprehend it. Don Casey's Complete Illustrated Sailboat Maintenance Manual
and/or Nigel Calder's Boatowner's Mechanical and Electrical Manual
would be excellent places to start, AND they would cost far less than you have already spent on electrical work.