Draft: Correct the moment of flags deliver to HypoTools

Before we can generalise the HypoTool generators to return CAs (followup of the MR: !61930 (merged)) we need to fix the place/moment where the flags are taken to hypo tools. Providing them via menu package is a mistake. It is because the flags may potentially be customised through cloneAndReplace in signature codes. This MR is supposed to fix them. The change is trivial but quite widespread.

Tagging @fwinkl & @fpastore

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