Learn English – How etiquettical is it to start off a professional email with ‘Hey’

In theory, this should be easy. Drop "deceptively" and you have the essential quality of the subject:

"The floor is deceptively flat" → The floor is flat.
"He's deceptively strong" → He is strong.
"He looks deceptively strong" → He looks strong.

Now add "deceptively" back in to indicate how the observer has been deceived:

"The floor is deceptively flat" → The floor is flat (but appears otherwise).
"He's deceptively strong" → He is strong (but appears otherwise).
"He looks deceptively strong" → He looks strong (but is otherwise).

The difference between #2 and #3 is the difference between "looks" and "is." This has the effect of flipping the comparison around: in #2, you are deceived about how he is, and in #3 you are deceived about how he looks.

In theory, it's easy. In practice, you're just as likely to find the word used to exactly the opposite effect, so in most cases you should assume you're going to need to get the meaning from context. I'd recommend staying away from "deceptively" entirely when writing: "The floor is flatter than it looks."

The natural phrase is "Bear X in mind", the other construction always a second choice.

The X is a direct object, and English prefers to put direct and indirect objects without prepositions before prepositional phrases: "Give John the book", but "Give the book to John".

On the other hand, we also do not like to put the parts of uncommon idioms too far apart.

This particular idiom tends to take phrases in 'that' or 'whether', which are hard to get out of cleanly. So we push those to the end, after the prepositional phrase that closes idioms of this form, to avoid confusion.

I would go with "Bear theorems [1] and [2] in mind" because it does not have this closing-a-phrase problem. But "Bear in mind that blah, blah blah."