is the 90 days/year 270 days/3 years rule inflexible?

[gascoyne]

I found some information on this here but it was a few years ago. My situation is that my wife, a national of another EU country, wants to apply in addition for a UK passport: she is worried that because we spend around 3-4 months each year in total abroad at a 2nd home in the EU (not her homeland) her application might be rejected.
I see from Home Office guidance booklet "Nationality policy: assessing ordinary residence" that there seems to be some flexibility. For example, it is stated that "ordinary residence is established if there is a regular habitual mode of life in a particular place for the time being , whether of short or long duration, the continuity of which has persisted apart from temporary or occasional absences, residence must be both voluntary and adopted for a settled purpose".
My wife is certainly settled and ordinarily resident, having lived in England for 30 years (for most of which time she's been married to me), was granted right of permanent residnce over 20 years ago, jointly owns our marital home, is established in her UK profession, and we have a son who was born here and resides here.
Is there any other reassurance or guidance or whatever than anyone can offer?
Many thanks, G

[secret.simon]

Pages 16-17 of the Nationality Guidance on naturalisation state how the discretion on absences in the naturalisation qualification period is exercised.

Discretion is more likely to be exercised if the absence was caused by events outside the applicant's control (such as an Icelandic volcano erupting when the applicant was aboard, making it harder to get to the UK, or a serious accident while abroad necessitating an extensive period of no travel) and its frequency (was it a one-off?).

In your wife's case, the fact that the absences were regular and voluntary may count against discretion being exercised. However, having a family and property in the UK may count in her favour.

[gascoyne]

Thanks SS, that's useful to know (+ the link) though somewhat discouraging: given my wife's having lived rather longer in UK than in her homeland and is thoroughly established, it seems odd to me that absence from the country brought about by holidays might count against her application for naturalisation. It's not as if she's spending time back in her homeland either: our 2nd/holiday home is elsewhere and we visit it together specifically for holidays... Still, if that's the rule, maybe this year we can arrange things so that she does not exceed 90 days away.
Thanks again - G

[gascoyne]

..Still, if that's the rule, maybe this year we can arrange things so that she does not exceed 90 days away.

I should have added to this, how might we prove subsequently that my wife has not exceeded 90 days out of UK in the preceding year? Does the Home Office maintain this sort of data on file, from those passport-readers at ports/airports? Or do we need to provide affidavits from neighbours, or something? I know nothing about these things...
rgds G