The answer to why it is not a good idea to split a battery bank lies in basic HS physics, which in my case took awhile to surface after a half century of neglect.
The basic issue is resistance in parallel and how current flows through a circuit, not the voltage drop. Electrons are lazy and will take the shortest path with the least resistance.
In a series circuit total resistance is easy to calculate, just add up all the resistance and you get a total. In a parallel circuit resistance is a little trickier to calculate. (BTW, it is all based on Ohms Law I=ER, see link below for the algebra.)
The formula for resistance in a parallel circuit is Rt =1/R1 + 1/R2 + 1/R3 ... where Rt is the total resistance and R1, etc is the resistance of each source, for this discussion, the internal resistance of a battery.
Let's assume the three batteries in the bank have a resistance of 100 ohms each. The total resistance for the circuit will be 1/100 + 1/100 + 1/100 = 3/100 or .03 All the current passing through the bank will be equally shared between the batteries and thus all will be equally drained or charged. So long as the batteries are of the same type and condition life will be good. However, if the batteries are not equal, then the charging will not be equal. This is why it is recommended to replace all the batteries in a bank at one time with the same type of battery. It is also why jumpers need to be of the same length as the resistance of the longer cables will increase the resistance in the circuit resulting in more current going to the battery with lower resistance, the first battery.
The wiring scheme the OP proposes is still in parallel with one important difference, functionally he will have 2 separate banks with one bank having one battery (Bank 1) and the other having two batteries (Bank 2).
Calculating the resistance in the circuit:
Rt = 1/Rb1 + 1/Rb2
Solving:
Rt = 1/100 + 1/((1/100)+(1/100))
Rt = .01 + .02
Rt = .03
Notice Bank 2 now has twice the resistance of Bank 1 which means it will accept less current than Bank 1. If the charging source is allowed to fully charge all of the batteries to 100% SOC, it is probably not a big deal. As Bank 1 approaches 100% SOC the internal resistance will increase and more of the current will then shift to Bank 2 until it is at 100% SOC. However, in practice most of us do not charge our batteries to 100% every time they are partially discharged. If charging is stopped before Bank 2 is fully charged, Bank 1 will discharge into Bank 2 until they are all equally charged. Functionally, this increases the number of charge/discharge cycles for Bank 1 relative to Bank 2.
Because Bank 1 has a lower internal resistance than Bank 2, when discharging more amperage will come from Bank 1 than Bank 2, resulting in deeper discharge levels in Bank 1 than Bank 2 which increases the cycles relative to Bank 2. More cycles and deeper discharges results in shorter battery life, especially for LA batteries.
Unequal jumper cables will add to the resistance calculations. An 18" jumper will have 3 times the resistance of a 6" jumper resulting in less current being sent to the battery at the end of the 18" cable. With all cables the same length the current distribution will be equal, with equal resistance to each battery charging and discharging will be even across the individual batteries in the bank. Which is the goal.
To summarize, restricting current flow because of resistance is the key issue when designing a parallel battery system. Proper wiring with the correct sized cable for jumpers of equal length will yield more efficient performance and increased battery life.
