This BMS does limit the alternator charge current depending on the fuse chosen. From the product description.
The dedicated alternator input provides current limiting and one-way traffic from the alternator into the battery, this so any size alternator (and start battery) can be safely connected to the Smart Lithium battery or batteries.
Have a look on the product page and read the manual.
https://www.victronenergy.com/battery-management-systems/smart-bms-current-limiter
I do not know about having the loads on the MPPT as these may not be shut down, you may need to fit some form of isolation such as a cyrix relay on the loads. Hopefully someone else can answer this part of your question.
The only thing to be sure of is if you have a smart alternator that varies the charge vo!tage. You need to make sure your alternator delivers 14.5V or thereabouts to allow for some voltage drop in the BMS.
See link for some notes on this
https://community.victronenergy.com/t/smart-bms-12-200-or-bms-cl12-100-alternator-charge-current-is-much-lower-than-the-fuse-value/93