Both sentences are systematically ambiguous.
They each contain a modal auxiliary (must, may) and a negative quantifier (only).
This mix of operators in one proposition inevitably produces ambiguity.
Further, only is the kind of quantifier that binds a focus. (1) below is ambiguous between (2) and (3), with different focus.
- He only [drinks dark beer on Tuesdays].
- He drinks only [dark beer] on Tuesdays.
- He drinks dark beer [on Tuesdays] only.
This is because words that bind a focus can appear right before the focus word (or right after, especially at the end of the sentence), or they can appear right before any constituent phrase or clause that contains the focus, so (1) could refer to either (2) or (3), or to their combination, which is yet another phrase.
That's just one of the complexities of only. The modals add several other dimensions.
With generic you (i.e, the reader) as a subject, may only have one account is deontic (i.e, it refers to social obligation/permission, not logical necessity/possibility). And it means that you must not have more than one account. It does not mean that you must have an account at all; just no more than one.
Must only have one account, is also deontic; however, it requires that you have no more than one account, and also requires that you have an account.
So they're not quite the same. I should add that the distinction is minuscule, and probably limited to this particular context and construction type. Like I said, the phenomenon is much more complex semantically than it may appear.