3rd country citizen married to EEA applying for nationality

Esteemed members,

I will upfront apologise if this has been discussed before and if there are any topic links I am more than happy to read up. I have already been looking at General discussion on CSI and Settled Status. Big issues for people on the EEA-Applications Routes and csi-and-settle-status-big-issues-for-everybody but did not find anything that would be a precise fit.

My wife which is a 3rd country national is applying for British nationality and initially it looked as if she complied with all requirements but following applying (docs not submitted and biometrics appointment is not until end of Jan 2021 but application paid) I find more and more caveats with the application and becoming uncertain if she should withdraw the application before it is too late for a refund.
The naturalisation application was made using Indefinite Leave to Remain (ILR) under Appendix EU to the Immigration Rules.

Facts
EEA national arrived to the UK 3rd September 2003 and have been employed the entire period and still is to date. Have both EEA resident card and EEA permanent resident card as well as EU SS

EEA family member time line is
TYPE APPLICATION START DATE END DATE
1 | EEA Family permit 05/03/2013 08/03/2013 08/09/2013
2 | EEA resident CARD 12/03/2013 06/09/2013 06/09/2018
3 | EEA Perm resident CARD 12/03/2018 08/06/2018 08/06/2028
4 | Indefinite leave to Remain Indefinite Leave to Remain (ILR) under Appendix EU to the Immigration Rules. AKA EU settled status; 10/02/2019 10/02/2019 Indef.
5 | EU scheme settlement CARD with substitution biometric residence card reissued due to theft of card
23/09/2020 09/12/2020 09/12/2030
If you see the application dates for EEA Permanent resident card I actually applied before the resident card expired under the pretext that the date of arrival to the UK is what counts and not the issue date of the EEA resident card. In any case there is my first hurdle; I may be incorrect in my interpretation of the law. And if so, my wife may potentially not have been entitled to a permanent resident card until the 06/09/2018 while it was actually issued 6 months early i.e. 12/03/2018 and it could be claimed she obtained the permit by fraud.
Then the problems follow as although the expiry date of the resident card is 06/09/2018 and one applied exactly on the expiry date and assume the HO takes the max allowable time to issue the permanent resident card (6 month) the card would have been issued 06/03/2019 but my wife applied before that date for EU SS the above in that she may not have been entitled to register under EU SS which was on the 10/02/2019 and that is aprox 1 month too early if had we followed the issue date instead of the application date. So again it could be claimed that the EU SS had been obtained before she was actually entitled.
One could also assume the stance that HO had issued the EU SS and it should have been obvious both during application for permeant residence card and EU SS that the dates did not square up.
In that case what would the arguments be? HO did not doo due diligence which is none of the applicant's fault? Or will HO claim the docs were obtained fraudulently? Or is there no mistake as my assumption with application dates is valid?

If the above does not pose any issue then there may be an CSI problem.
Period
1 | No activities but then if my interpretation above stands she would be an EEA family member under EEA2 application and could have had CSI while studying although it seems that rule was implements much later
2.| Studying English however no CSI from the date she arrived in the UK to when she registered as self employed June 2015 and some periods as employed while also being self employed.
3 | Studying English and self employed and some periods also being self employed
4 | Studying English and self employed and some periods also being self employed
5 | Studying in Uni and self employed.

So, if she should have had CSI should I request that the Home office, when they consider the application, include all the facts surrounding the CSI breach and make a full assessment about whether discretion should be exercised in my wife's favour? Or is it better just to keep shut and raise the matter if the application is refused?

Or, is she in fact lawfully settled as she obtained as her self employed dates would then be June 2015 to June 2020 an d her settled status period free of 10/02/2019 and even if the dates should be corrected that would make that the settled date as any time spent in the UK “in breach of immigration law” does not count towards the qualifying residence period.
Or perhaps there is no issue at all!? Because she is a EEA family member and the first 5 years when she is on EEA 2 i.e residence card she would depend on my EEA activities and I was employed from the very day she arrived to the UK?

Looking at british-citizenship/csi-and-settle-stat ... l#p1901210
You must assess whether the individual has been here lawfully during their 3 or 5 year residential period prior to pre-settled status or settled status, by considering on the balance of probabilities whether they were here:
• as a qualified person (such as a worker, student, self-employed, self-sufficient, retired or incapacitated person)
• as the family member of such a person. (That would be reference to the EEA national)

Which makes the next sentence void as that would only apply if the EEA national has not been employed or self employed or had CSI for both parties.
Evidence of this can include API data or documents previously submitted to satisfy their lawful residence. Where appropriate, you must also be satisfied that the person was lawfully in the UK, with comprehensive sickness insurance (CSI).

Am I totally down the wrong lane here?

Many thanks and happy New Year to all of you,
Michael

Correction

Under Facts it should read
Have both EEA resident card and EEA permanent resident card as well as EU SS.

Not sure how my original text was warped into Surrinder Singh.