The argument here seems to be that s 23 (1) of the European Union (Withdrawal) Act 2018 gives a general power to ministers to modify any provision under any enactment (including enactments passed within the same session of parliament) legislation.gov.uk/ukpga/2018/16/…

If such an order is made it is to be made in accordance with Sch 7 of the 2018 Act
legislation.gov.uk/ukpga/2018/16/…

It does not seem that the power to remedy deficiencies could be used under s 8 of the Act as regs under that provision are to fix to issues of retained EU law
legislation.gov.uk/ukpga/2018/16/…

Sch 7 para 15 means any regulation made under s 23 and not positively approved by parliament but can be subject to annulment by Parliament (ie they can vote against it) where the para 17 procedural limits are complied with legislation.gov.uk/ukpga/2018/16/…

Sch 7 para 19 allows a regulation to laid without being approved by parliament in cases of urgency. However, any attempt to do so requires the minister to comply with Sch 7 para 34 explaining why it must be made urgently.

Any regulations made under s 23 of the 2018 Act though require to be "in consequence of " the 2018 Act. This Act contains various provisions regarding parliamentary approval of a withdrawal agreement (which is also the basis of the later 2019 Act?

Would an order to prevent a negotiated agreement or the failure to obtain a negotiated agreement be in consequence of the 2018 Act?

Also, how does the European Union WIthdrawal (No 2) Act 2019 sit with the 2018 Act? Could it be argued that the general power to modify legislation under s 23(1) of the 2018 Act is subject to the doctrine of implied repeal?

Ordinarily in parliament legislation which comes most recently can prevail as any later legislation can amend or vary earlier legislation. However, there are complications where the later legislation is silent on the interaction with earlier legislation

Where legislation is so inconsistent that two pieces of legislation cannot be read together or they are repugnant then the later legislation can impliedly repeal the former (to the exent to which they are incompatible).

While there is a presumption against implied repeal (and there is a statement in the case of H v Lord Advocate [2012]UKSC 24 that implied repeal is not possible for constitutional statutes (which would include the Scotland Act 1998 but how much further?))

But while the presumption tends to apply where there is specific earlier legislation which contradicts general later legislation the reverse is true where there is a high level of specificity in the later legislation. (R v Director of SFO ex p Smith [1993] AC 1)

in this case as well as the problem with any SI to block the 2019 Act falling within the scope of the powers under s 23 of the 2018 ACt, the level of detail in the 2019 Act would suggest, I think, that an implied repeal argument (to the extent of the 2019 Act) is stateable