With SYSTEM_THREAD(ENABLED) the impact on your code with SYSTEM_MODE(MANUAL) isn’t too breat.
While the docs mention that your code needs to explicitly call Particle.process() that’s only true if you are not running SYSTEM_THREAD(ENABLED) - AFAICT.
Since you are already running SEMI_AUTOMATIC all the necessary steps should be in place. One difference betweem SEMI_AUTOMATIC and MANUAL with SYSTEM_THREAD(ENABLED) is that some functions are non-blocking in MANUAL mode while they are (under some circumstances) in SEMI_AUTOMATIC mode.
(I see I’m repeating myself, I didn’t follow the link in @Rftop’s post before answering 
)