question

On the first question, yes the output current limit of the controller will restrict power. Your calc is not correct for batteries in series. Use the serial voltage. E.g. 39V in your example. Be aware that SOC of the batteries and light levels will also affect output.

On the second question, usual advice is to follow maker's instructions. Failing that max discharge of 50%. It's a trade off to minimise battery cost. The lower the voltage you discharge to, the shorter the service life/number of discharge cycles. It would be interesting to see the expected discharge cycles to this level compared to 50%. Time before recharge also has a big effect.

You wrote that the batteries are in series (to 36V) but on the picture is looks like they are in parallel (12V).

In that case you are limited to around 250-300W charging power.

You need a bigger MPPT or a second one.

290W @ 12V (20A * 14.5V):

Those are about 110Ah batteries meaning they should be charged with about 11A max per battery in parallel (you said series, but they are in parallel), so the most you want to charge with is ~33A - that's about 2 of those panels on a controller that can handle > 33A.

Voltage cut offs are tricky. The voltages that reference to % charge are always for RESTING voltage, i.e., a battery that hasn't been charged or discharged for 10-24 hours depending on specification. If you cut a battery off at 12.05V while under load, the battery voltage will rebound. If the goal is to limit the battery to 50% discharge, the best thing is to get a BMV/Smartshunt programmed for 330Ah and then figure out where your voltage is when it reads 50% - use that as a cut off.

IMHO, best option would be to add a 4th battery, add the second 100/20 and put two panels on each 100/20 yielding 40A of charging against 440Ah of capacity.