If Statutory Instruments are (sometimes?/always?) used to enact Acts of Parliament
In particular, they tend to be used to specify details (e.g. regulations) that would be too cumbersome to be included in an Act, and which might change over time. They are also commonly used to bring Acts, or parts of Acts, into force on particular dates (commencement orders).
are their powers bounded to maintain democratic legitimacy?
Well, it's a matter of legal theory, in that a government has only the powers which Parliament grants it (apart from the Royal Prerogative).
Are there any controls in place to avoid Statutory Instruments - that can effectively bypass Parliament - from “overreaching”?
Yes. Unlike Acts of Parliament, SIs can be nullified by the courts.