Bootloader GPIO Issues

## Bug report

**Issue details**

After a lot of triaging, it seems the new SD card based flashing stuff in 4.5+ (maybe older?) breaks the bootloader's ability to handle GPIO correctly?
In my case, I noticed the issue when peripherals that normally are off during boot started working. For example: `PD15 VDD_5V_PERIPH_EN OUTPUT LOW` does not hold PD15 low. It's high or floating.

Specifically, when these lines (perhaps only some are needed) are enabled in my bootloader hwdef, this issue exists.

```
# enable flashing from SD card:
# microSD support
PC8 SDMMC1_D0 SDMMC1
PC9 SDMMC1_D1 SDMMC1
PC10 SDMMC1_D2 SDMMC1
PC11 SDMMC1_D3 SDMMC1
PC12 SDMMC1_CK SDMMC1
PD2 SDMMC1_CMD SDMMC1
# enable FAT filesystem support (needs a microSD defined via SDMMC)
define HAL_OS_FATFS_IO 1
define AP_BOOTLOADER_FLASH_FROM_SD_ENABLED 1

# FATFS support:
define CH_CFG_USE_MEMCORE 1
define CH_CFG_USE_HEAP 1
define CH_CFG_USE_SEMAPHORES 0
define CH_CFG_USE_MUTEXES 1
define CH_CFG_USE_DYNAMIC 1
define CH_CFG_USE_WAITEXIT 1
define CH_CFG_USE_REGISTRY 1
```

**STR**
```
./waf distclean
./Tools/scripts/build_bootloaders.py
./waf configure --board=
./waf copter
```

**Version**
4.54+ (whatever version started supporting flash based firmware updates I suspect)

**Platform**
[ x ] All
[ ] AntennaTracker
[ ] Copter
[ ] Plane
[ ] Rover
[ ] Submarine

**Airframe type**
_What type of airframe (flying wing, glider, hex, Y6, octa etc)_
n/a

**Hardware type**
_What autopilot hardware was used? (Pixhawk, Cube, Pixracer, Navio2, etc)_
Custom

**Logs**
_Please provide a link to any relevant logs that show the issue_
n/a

Start by reproducing the listed bootloader and Copter build commands with the SDMMC1, FATFS, and GPIO settings in the bootloader hwdef. Trace bootloader GPIO initialization alongside SD-card flashing support; done means PD15 reliably remains low during boot while SD-card firmware updates continue to work.

Written by the indexing model from the issue text.