I can see in mkr1000/variant.h that SERCOM4 is used for WiFi IC communications. From the diagram in the ATSAMW25 datasheet http://ww1.microchip.com/downloads/en/devicedoc/atmel-42395-smartconnect-atsamw25-mr210pa_datasheet.pdf, it looks like there's an interrupt line from the WiFi module to the microcontroller labelled "IRQn". This is similar to another SPI slave device I've read about that uses the interrupt to initiate data transfer to the SPI master, so I assume it's being used. If Arduino does in fact use interrupts this way, where does the Arduino core or library set the interrupt handler? I can see in Arduino/libraries/WiFi101/src/bsp/source/nm_bsp_arduino.c that there is a modified facility to set the interrupt handler, but I can't find where it's being called (if it's being called at all).
Whew! I think I found it! In the Arduino WiFi101 library source, WiFi.begin() calls WiFi.init(), which calls m2m_wifi_init() which calls hif_init() which calls nm_bsp_register_isr() which calls attachInterruptMultiArch(). I can't say I understand what the ISR is doing (yet), but it seems to be in m2m_hif.c.
I think the big picture is this: the Arduino library builds on the code from Microchip, and that code seems to be pretty well documented here http://ww1.microchip.com/downloads/en/devicedoc/atmel-42420-winc1500-software-design-guide_userguide.pdf