My colleague was able to enter the uf2 mode programmatically using the same calls as Meshtastic.
The only difference is the bootloader version on our T1000 devices
On my device the UF2_INFO.TXT reads:
UF2 Bootloader 1.00
Model: Seeed T1000-E for LoRaWAN
Board-ID: nRF52840-T1000-E-v1
His reads
UF2 Bootloader 0.9.1-5-g488711a lib/nrfx (v2.0.0) lib/tinyusb (0.12.0-145-g9775e7691) lib/uf2 (remotes/origin/configupdate-9-gadbb8c7)
Model: Seeed T1000-E for Meshtastic
Board-ID: nRF52840-T1000-E-v1
Date: Jul 15 2024
SoftDevice: S140 7.3.0
This must be the smoking gun