When combined the two batteries become one large battery.
Yes, the batteries will discharge from one to the other until both batteries are the same voltage (equalize), but that’s it.
You're spot on right..........100% and because I can't sleep..............
This is the stop were I always will get off the bus...........Paralleling (combining, either automagically with a ACR/VSR or with the manual "Off, 1, Both, 2" batt switch) the needed kept in reserved "safe" start battery with a discharged'ish house battery
isn't best practice.........Not in my boat anyway and typically, not in any industry were preserving reserved energy at specific potentials for power needs are required/desired to do optimal work.......
This "equalization" after combining/paralleling is effectively just discharging your topped off start batt into a depleted house batt., the net result is as you state, "one big battery" BUT, and as I agree, and as I also see it in the following example, instead of having your start batt *kept safely at or around a 13V potential along with having a discharged house batt at say 11V, I would definitely agree, after combining, we now have one big battery, with say 12V or less!
"12V or less" as the example goes, is of course dependent on how discharged the house batt was at the time of combining, the capacity of each individual battery and SOC on the start batt, obviously..........Plus several more variables would dictate an exact value, however.......
This net effect happens because the alternator (the third voltage source) at the time when the two batteries are combined, can't supply (current limited voltage source) enough current due to the fact the depleted battery/ies instantaneous(di/dt)/inrush current draw reaches up to several several hundreds of amps and can take a bit of time to normalize. The alternator's output now has a **voltage drop out/sag that is forced down to the combined battery voltage due to being max'd out (12V in our example case).
So now, the "one big battery" of 12V, in this example, now takes time (can be hours and dependent on the alternator output amp rating) for the one big battery to come back up to say 13.8V-14.2V.
In a nut shell?.......Given a house batt being discharged at some level, when paralleled with a fully charged start batt, the action of paralleling sucks both the alternator (current limited voltage source) and the start battery down to 12V until the alternator can recover given some time by charging now BOTH (twice the capacity due to being paralleled) batteries back up
Given this........
It is always best practice, to leave the charged battery charged and re-charge JUST the low battery by itself. And as such, I prefer an battery management system that prevent this "back charging" as its called......
A diode isolator that is voltage bias up using the alt's (mag or armature type) sense lines to make up for the diode drop (either silicon 0.5V or schottkey 0.2V) is easily done and works fine or use a smart switching battery "zero drop" management device (FET or Relay), those also work very well.
If you use a "Off, 1, Both, 2" batt switch and can remember well (I always forgot), switch over to house (2) when stopped, use what you went, then switch over to start (1) to start. Once started and the start batt is topped off (few minutes), manually switch back to house (2) and NOT combined. Let the house come up to roughly what the kept safe start battery is at (13V in our example), then you may if you want go to "both"
Of course, all this is just my opinion (and an industry accepted best practice approach) and has worked best for my needs and has worked quite well over the many years I've used this type/s of setup. Individual taste and preferences always apply here. And just like elbows and.......well, you know .
*recalling starters require power to function as designed and because P=I*V, keeping the voltage "V" (13V) magnitude higher is important here at a given curret "I" (given due to the fixed R in the starter's winding's) for power "P" to remain high enough for the starter to spin up and
do work at the required rates (Specifically Sim 1 verse Sim 2)
**this is why ACR/VSR's require
hysteresis, it helps prevent self switching on and off oscillations at combine time due to this a rapid drop in voltage when paralleled, then due to it dropping to far, it un-combined, hence, it became an oscillator. At one point I recall; the older ACR's didn't have enough hysteresis and were known to oscillate quite a bit at combine time, they since had a rev or two and have up'd the original hysteresis thresholds even more due to this very prominent dropping out/ voltage sagging that occurs when a depleted battery is paralleled with the good battery.