There are at least 2 issues here.
Firstly, in the case brought by Gina Miller, the Supreme Court ruled that the government could not rely on Royal Prerogative and needed an Act of Parliament to actually withdraw from the EU. Clearly the government did not have the authority to revise the leaving date without going back to the HoC. It is technically 'illegal' in the sense that the government is doing it the wrong way around: they have already requested the deferment and will now place the Statutory Instrument in front of the HoC (tomorrow) for approval to validate what the government has already done.
But as you point out EU law trumps UK law and the EU has already turned the deferment into EU law… so the UK cannot now leave on 29 March! Because EU law says so!
Thus even if the HoC were to vote aginst the SI tomorrow, it would have no effect… the UK is bound by EU law.
What now happens if the EU decides it needs more time to prepare for Brexit and the other 27 agree that the leave date should be further deferred until… say, 25 August 2035… or any other date. They have already changed the date on the basis of an illegal act by HMG… so quite clealy there was no procedure they had to compy with before changing the date for the first time.