Using your config files I cannot replicate this issue on current bugfix.
compare the start of compile to this
PLATFORM: Atmel AVR (2.2.0) > Arduino Mega or Mega 2560 ATmega2560 (Mega 2560)
HARDWARE: ATMEGA2560 16MHz, 8KB RAM, 248KB Flash
DEBUG: Current (simavr) On-board (simavr)
PACKAGES:
- framework-arduino-avr 5.0.0
- toolchain-atmelavr 1.50400.190710 (5.4.0)
Converting Marlin.ino
LDF: Library Dependency Finder -> [bit.ly]
LDF Modes: Finder ~ chain, Compatibility ~ soft
Found 10 compatible libraries
Scanning dependencies...
Dependency Graph
|-- <U8glib-HAL> 0.4.1
| |-- <Wire> 1.0
| |-- <SPI> 1.0
|-- <Wire> 1.0
|-- <SPI> 1.0
|-- <EEPROM> 2.0
|-- <SoftwareSerial> 1.0
Building in release mode