There are not many people that use SPI for primary interaction with the ESP8266. It's very well possible though, indeed.
If you are relating from a computer point of view then certainly UART is the best way to communicate with the ESP8266 - but between embedded ICs, SPI certainly has higher bandwidth (considering 80MHz SPI-Clock you are able to transmit 80Mbit/s).
Only one SPI module can be used, the other one is for accessing the flash memory.
If opened another topic about the SPI used for flash:
viewtopic.php?f=13&t=20702 just a few days ago.
And @btidey mentioned that it sure is possible to share the Flash-SPI with other devices (even though CS0 has highest priority, but CS1/CS2 could be used in theory, practically you don't want to re-map the functionality of CS1 which is the UART-TX used for flashing, so you are left with CS2).
I don't see the use though as there is already a second SPI controller provided.
You are right, it is much easier to just use the second SPI block.
But also in that case you wouldn't be using, imho, the unique selling point of the device.
Think about it that way: The main selling point of the ESP8266 would shift from being a low-price WIFI-enabled controller to a low-price high-speed controller (considering that the ESP8266EX IC is available via Taobao for as low as ~40 Euro-Cent, there is just no other device running at >300MHz for 40 Cent).
I would appreciate it very much if anyone could share his/her experience with the ESP8266's PLL.