How are you going to flash it from the IDE without Trinketboot?
And what are you trying to build? From what source?
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The error you are getting with FUSEEBIN not declared in this scope is because you are not "#include"-ing the correct .h file.
Trinketboot does not need to show up as a disk drive in order to flash. That is an additional feature provided by the UF2 bootloader for easier (non usb) programming. Loading arduino via the main.ino, compiling and uploading (ctrl + U) is the way that I flash my devices. The device shows up as a trinketboot UF2 in device manager > ports, and assigns a port, so Arduino can flash just fine.
I am trying to build from your files that you provided on your github, aka 'version 2', here -
https://github.com/mattytrog/GBATEM..._REBUG_SwitchME/TRINKET_REBUG_CHAINLOADER.zip
Regarding the not including the correct .h file, I have payload.h and usb_setup.h in the main folder (as your zip includes), as well as the pre-requisites libraries installed as specified in your OP. What .h file am I missing? I only changed the various payload options in the main.ino, I did not change anything else.
Here is the only section that I made alterations to.... I didn't think changing any of those would cause the specific error?
// Sam_fusee_launcher - Credits to quantum_cross for original code
// Mattytrogs multi-payload
#include <Arduino.h>
#include <Usb.h>
#include <Adafruit_DotStar.h>
#include <FlashStorage.h>
//CHANGEABLE VALUES!!! CHANGE THE VALUES BELOW TO YOUR LIKING
#define AMOUNT_OF_PAYLOADS 1 //set number of payloads required. 1 - 8.
#define AUTO_INCREASE_PAYLOAD_on 0 //Automatic increase payload when send fails. 1 = on, 0 = off
#define AUTO_SEND_ON_PAYLOAD_INCREASE_PIN 0 // Automatic send when payload pin is activated. 1 = on, 0 = off
#define FLASH_BEFORE_SEND_on 0 // flash payload number before attempting to send. 1 = on, 0 = off
#define FLASH_AFTER_SEND_on 1 // flash payload number after send/attempted. Will show same payload number(if autoincrease is off, or next payload number) 1 = on, 0 = off
#define LOOK_FOR_TEGRA_SECONDS 5 // how long to look for Tegra for & flash LED in search phase. Time in seconds
#define LOOK_FOR_TEGRA_LED_SPEED 100 // how fast to blink when searching.
#define DELAY_BEFORE_FLASH_WRITE_SECONDS 2 //get out of jail card. Press reset during this time and payload won`t be increased