No, you should not bypass the BMS without some form of protection. Will did do a trick where he used a lower current BMS, but had it's output lead drive a contactor that connected the inverter to the system, but this would also work for the charge controller. The whole point of a BMS is to protect all of the cells from over voltage, under voltage, over current, and temperature extremes. When using the relay bypass trick, it does eliminate the current protection, but you can (and should) still have a fuse or breaker to limit the maximum current incase something goes wrong. The rest of the protection systems still work because when the BMS goes open, it drops the contactor (relay) and shuts off the load or charger. If you were going to do the relay trick, I would recommend a separate port BMS and 2 relays. One for the charger, and one for the load. This way if it runs low, it can still charge, and if it goes too high, the loads can still pull it down.
When using a common port BMS, the inverter, charger, and any other loads, should all connect on the output lead of the BMS. Mine is a common port that allowed me to set different maximum current for charge and discharge direction. And even though it is on the same physical wire, it can block charge when the voltage is high, or block load when the voltage is low, but still allow the other direction so a low batt can be charged etc.
The SCC should be set for the whole pack voltage. Set it a couple tenths of a volt below the desired max cell voltage times the number of cells. In my case, I have MNC cells that are safe to 4.2 volts. I have 14 in series for a max voltage of 58.8 volts, but I have my absorption voltage set to 57.6 volts, which works out to 4.117 volts per cell. Add in a little wire voltage drop, the BMS drop, and some calibration error, and my BMS reports right at 4.1 volts per cell when the charger stops. The BMS will not disconnect until 4.2 volts. on a cell. On the low side, I am even more conservative. I have the inverter shutting off at 44 volts, which is still 3.2143 volts per cell. The BMS is set to 3.0 volts per cell, or just 42 volts for the pack.