I have a similar concern about the Adrenaline Pump, which boosts Strength, Agility and Reaction (and Willpower). RAW that's incompatible with Muscle Toner, Muscle Augmentation, Wired Reflexes, Synaptic Booster & Reaction Enhancers.
The exception appears to be Muscle Replacement, which could generously be read as compatible with Adrenaline Pump and Superthyroid Gland because it says "
it cannot be combined with other augmentations to the muscles
" my emphasis.
And yet Adrenaline Pump and Superthyroid Gland make no mention of being incompatible with anything. Including each other.
There appear to be three or more different restrictions on combining things here. Some to everything (magic included), some to Augmentations and some to certain types of Augmentations.
It seems sensible to rule that Adrenaline Pump and Superthyroid Gland stack with everything, because they have no restrictions in their description and they are gland / chemical based, not actual replacement / enhancement of the thing you're trying to effect. I could see an argument not to stack with cyber because it isn't really natural, but not bioware. I presume the augmented maximum would still apply, so it's not like you could be a human with Agility 6 (Muscle Toner R3 - 9), Adrenaline Pump R4 to boost to 13. (yikes the crash on that is going to hurt)