Hi Sam,
I can answer two of your above questions for you. Question 1... yes, I'm using QSPI on the alternative pinmux. See my comment above this one that has the MCU Boot Utility settings I use with my RT1052 and IS25LP064A QSPI flash on the secondary pinmux location.
Question 2... I rather suspect there should be some activity when the serial bootloader starts. There should also be activity if you've selected Internal Boot. Based on my own experiences trying to get a different model of QSPI flash to work (before giving up and just using the IS25LP064A), I strongly suggest that you make sure you've got your bootstrap settings correct.
On our custom RT1052 Rev. A board, we fully replicated the boot select switches that are found on the RT1050 EVKB. Here's a snap of the schematic page:

And here's an annotated copy of the BOOT_CFG[11:0] and BOOT_MODE[1:0] bit definitions:

Please note... the 12 boot switches do not correspond directly to the 12 BOOT_CFG bits. For my BOOT_CFG[11:0], the only bits I have to set are bits 8, 9, and 10. Here's what my boot switches look like properly configured:

Selecting the secondary pinmux requires setting SW3-3, SW3-4, and SW4-2 (as pictured above). The last two switches correspond to the boot mode. On the RT1050, BOOT_MODE = 01 selects Serial Downloader, and BOOT_MODE = 10 selects Internal Boot. So above, the board is selecting Internal Boot. Note that on the RT1050 EVKB, the first two banks of switches are depopulated, partly because one is expected to use the 1.8V HyperFlash.
You should be able to set your board for internal boot off your secondary pinmux, and after powerup/reset, you should see activity on your QSPI pins. If you don't, your bootstrap settings are not correct. Look at your boot pins and your high/low pull resistors; the only pins that should be pulled high are BOOT_CFG[8], BOOT_CFG[9], BOOT_CFG[10], and BOOT_MODE[1] (for internal boot); all others should be pulled low.
If you are getting signs of life on QSPI when you reset your board in internal boot mode, then that's a good sign that FLASH_TYPE has been successfully strapped to 111. Once that's working, try switching to serial downloader mode, set all of the config options I show above, and see if that works for you.
David R.