They are 2 separated SPI slaves. What is the difference is the library between using one or two Host USB shield? What is the difference between a common multiple slaves SPI usage?
The library is designed to handle just one board. If the design is made that way you cannot just connect a second board and expect the library to handle that as well. Because your hardware design is quite exotic (with the two shields) nobody did the work yet to change the software to include this use case. If you wanna use two USB host shields you gonna have to rewrite large parts of the library.