Both methods will work, but it kind of depends on how big your binary is.
Since the application firmware is limited to 128K bytes, you probably can’t have much more than 120K assuming the Particle firmware does not do anything else.
If you do a separate download, then you’re limited by the storage space on the device. For the Boron, this is probably around 1.8 Mbytes out of the 2 MB LittleFS flash file system to be safe.
If your binary is bigger than that, you’ll need to add external storage like an SD card or larger external SPI flash.
It’s definitely possible to download a large binary, such as by HTTP or direct TCP, then save it and use it to program a coprocessor, though that’s not built-in and you’ll need to write some custom code for it.