First of all, it won't be possible to apply before you come back to the UK< so you will need to finalise the absence count once you are back.
Your spouse can apply on her own merit (showing proof of residence for 5 years, so the 450 days absence limit applies) or as spouse of British citizen (showing proof of residence for 3 years, so the 270 days absence limit would apply). Please note that you need to make sure your spouse was in the UK on the day 5 years (or 3 years) before you apply.
May I ask exactly how many days did your spouse spend outside the UK in the last 12 months, last 3 years, and last 5 years?
This is what the guidance
Absences from the UK during your residential qualifying period will be considered in the following way:
6(1) application
5-year qualifying period 6(2) application
3-year qualifying period (applicants married to, in a civil partnership with, a British citizen)
Normal permitted absences in qualifying period 450 days 270 days
Total number of absences normally disregarded. 480 days 300 days
Absences normally disregarded only if:
you meet all other requirements
and
you have established your home, family and a substantial part of your estate here. 900 days
Please note: if your absences are up to 730 days we would expect you to have been resident in the UK for the last 7 years.
For absences exceeding 730 days we would expect you to have been resident in the UK for the last 8 years unless the absences were a result of one of the reasons given below 540 days
Please note: if your absences are up to 450 days we would expect you to have been resident in the UK for the last 4 years.
For absences exceeding 450 days we would expect you to have been resident in the UK for the last 5 years unless the absences were the result of one of the reasons given below.
For absences exceeding 730 days (or 450 days for the 3-year route), please explain if your absences were a result of either:
A posting abroad in Crown or designated service (see the section on Crown and designated service). For example, as a member of HM Forces, or as the husband, wife or civil partner of a British citizen serving abroad in Crown or designated service
An unavoidable consequence of the nature of your work. For example, if you are a merchant seaman or someone working for a UK based business which requires frequent travel abroad
Exceptional or compelling reasons of an occupational or compassionate nature such as having a firm job offer for which British citizenship is a genuine requirement
The excess absences were because you were unable to return to the UK because of global pandemic
Only very rarely would we disregard absences in excess of 900 days (540 days for section 6(2) applications). If your absences are more than this limit your application is likely to fail and your fee will not be fully refunded.
Regarding absences in the last 12 months
In addition to the overall number of absences, you should not have been absent for more than 90 days during the final 12 months of the qualifying period. This applies to applications both under the 5- and 3-year routes.
Absences from the UK during the last 12 months of your qualifying period will be considered in the following way:
6(1) and 6(2) applications
Normal permitted absences in final 12 months of your qualifying period 90 days
Total number of absences normally disregarded 100 days
Total number of absences normally disregarded only if all other requirements are met and
you have demonstrated links with the UK through presence of family, and established home and a substantial part of your estate. 101 – 179 days
Total number of absences that may be disregarded if you do not meet all the other requirements providing the following criteria are met:
you have demonstrated links with the UK through presence of family, and established home and a substantial part of your estate
and
the absence is justified by Crown service or by compelling occupational or compassionate reasons taking account of the criteria listed on page 10
Please note that if your absences are high both overall and in the last 12 months it is probably best to wait until the absences in the last 12 months go below 90 days. If you comment more on your situation it would be easier to advise.
All advice comes from personal research and experience and should not be regarded as professional opinion.