As far as losing the Extra Attacks, that is because Mystra's Spells uses RAW version of Booming Blade. Whereby it doesn't trigger "Extra Attacks" because that only occurs when you use the normal "Attack" action rather than casting a spell (Even if said spell does involve an attack like Booming Blade)
As far as losing bonus action, this most likely is due to jank in how such things are implemented, where the attack involved in the spell is being counted.
When using Larian's Homebrewed Booming Blade, it will function with both Extra Attacks and War Magic. Enabling you to Booming Blade > Extra Attack(s) > War Magic Attack.
