Almost 2 years out of uk on spouse visa

Hello,
Dear Forum members,
We are in a confusing situation regarding my wife's spouse visa. In December 2020 I and my wife went to Pakistan in an Emergency due to my Late father's illness and then his death from Covid, also a few more very close relatives passed away one after another due to the pandemic during the same period. Then the uncertain situation of flight restrictions and later due to my wife's pregnancy and the birth of my son, we finally returned back to the UK in November 2022. If the above hadn't happened my wife would have been eligible for ILR in May 2023, but now I think she would need another extension for 2 years in order to complete her continuous 5 years on a spouse visa. My question is that let's say we get another extension of 2.5 years and then she gets ILR after 2 years, will it be possible for her to get UK citizenship as she will be absent for more than 90 days in the preceding 5 years before applying for citizenship?

Please share your valuable advice with me in this case.

You were given advice in 2021 when you asked similar questions with links to the guidance

immigration-for-family-members/stay-out ... l#p2036728