Is there a difference between must and may in limiting phrases?

No, "you may only have only one account" is not merely a suggestion. It is the preferred way to say this. It rules out the possibility of having two or more accounts.

"You must have only one account" would rule out the possibility of having no account at all.

must v. may

must TFD:

• 1. To be obliged or required by morality, law, or custom:
  2. To be compelled, as by a physical necessity or requirement:
  3. Used to express a command or admonition:
  4. To be determined to; have as a fixed resolve; inevitability or certainty; logical probability or presumptive certainty

and

may TFD

• 1. To be allowed or permitted to:
  2. Used to express possibility or probability:
  3. Used to express a desire or fervent wish:
  4. Used to express contingency, purpose,

Some overlap, some confusion, but in a contract: " you may only have one account" is not a suggestion. If you choose to enter into this contract you will (may) have one account.

If the "only" is removed from these sentences: "You may have one account" - permission. "You must have one account" - obligation. If "only" is added, You may only have one account = You must not have more than one account. The "must" is already implied in the sentence.

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.

1. He only [drinks dark beer on Tuesdays].
2. He drinks only [dark beer] on Tuesdays.
3. 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.