This is stopping me from going to sleep.
The similar Spell bonus depends on the magnitude of the the highest "similar" formulaic spell.
But Flexible Formulaic Magic can allow you to cast a known formula at 1 magnitude higher. Does this change in magnitude translate to the Similar Spell Bonus? It is keeping me awake trying to decide.
No. FFM allows you to adjust the spell level when casting a spell. It does not change at which level you know a spell, nor has it any effect on laboratory activities.
Psychology calls this motivated reasoning: My inner munchkin really wants to get to a certain conclusion. Therefor it manipulates my reason and reading skills to give a certain - false - meaning to the otherwise clear text. 
A good night's sleep lets me see how silly the question was. But last night I thought I had equally valid arguments both For and Against. Can't remember what they were now.
Sorry to disturb
The for is easy to see. You can cast 1 magnitude higher, so why not?
The against is the anti-munchkin inside just saying no.
To give a proper answer that isn't just "Muchkin begone".
RAW says in the Formulae review
'SIMILAR SPELL BONUS:
Magnitude of highest-level
similar spell known"
The 1 magnitude adjustment from FFM is an achievable affect, not how the spell is known.