Yes, you need to a) use Boot-style command-line arguments (which means -A alias1 -A alias2 rather than the clj-style of -A:alias1:alias2) and b) you have to explicitly tell boot-tools-deps that you really want to run the :main-opts rather than let Boot do its usual default runtime.
The latter makes it easier to work with aliases that both add dependencies and run code for clj, since you’ll often want to get the dependencies but still let Boot run code its own way.