mr/ms immibytes,
must be a Friday thing as am not exactly clear what you are after
My take is that:
1. Your partner came to the UK on presumably a 2 year Working Holiday Maker Visa - could you confirm this to be the case by checking what the stamp/ vignette on his/her passport says.
2. At the 18 month stage he/she got an ancestry visa which is valid for 4 years - could you confirm this to be the case by checking what the stamp/ vignette on his/her passport says. Is there a reason he/she did not apply for an AV before/ instead of the WHM.
3. You would like to travel but this is not so easy/ practical due to the visa requirements for South African nationals at the relevant destination.
4. You want to make such travel easier by your partner acquiring a British Passport.
If this is the case then note:
1. A WHM visa is
not in a category leading to settlement (CLS).
2. In contrast an AV visa
is is in a CLS so after 4 years consecutively on it he/she would be eligible to apply for Indefinite Leave To Remain in the UK using Form SET (O).
3. Form SET (O) like other settlement forms enquires as to the applicants absences from the UK for more than three months consecutively. Absences of over 3 months consecutively are considered to have broken your residence requirement for settlement purposes - this was implemented to stop people obtaining ILR despite spending hardly any time in the UK. The Home Office would exercise discretion where lengthy absences were for compassionate reasons e.g. family member abroad seriously ill and/ or employment with a British company which has seconded your partner overseas. They would also look at the ties in the UK during an absence such as having a property, paying taxes and National Insurance, Being registered with the NHS, maintaining membership of professional organisations etc.
6. Your partner has not been in a CLS for the required period of time. Even where he/she eventually does there may be issues around days consecutively outside the UK.
7. There is no limit to the number of AV's so he/she can apply for another one to make up the required residence time. As the immigration rules stand this would require a fresh AV application at an overseas British Diplomatic Post presumably the BHC Pretoria although an in country application could be made on a discretionary basis.
8. Once he/she has ILR and has held it for 12 month he/she would be eligible to apply for naturalisation as a British Citizen. He/she would need to meet the residence requirements amongst others i.e character, medical and language.
9. If the naturalisation application is successful he/she will be invited to attend a citizenship ceremony where he/she will swear/affirm an oath to the crown and be granted a certificate of naturalisation accompanied with a lovely cuppa

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10. He/she can then apply for a British Passport with the certificate as evidence of his/her British Citizenship.
however
1. You mention a 'we have not been together for two years' - i.e you are enquiring as to the possibility of an unmarried partner's visa which requires 2 years of a relationship akin to marriage on the date of application. You haven't got a chance with this as you don't meet the requirements and I fail to see any grounds to consider your case compassionatley outside the rules.
2. In any case a UP visa is initially for two years then apply for ILR then wait 1 year then apply for naturalisation then apply for BP as before so its not a faster route - If anything I would see it being slower. I would take Stonewall's comments at face value especially the part about waiting for the proposals on same sex couples not only being an operational policy but eventually making their way into the rules.
On a more positive note you will find that the authorities of the countries you intend to visit will be more likely to grant your partner a visa if he/she establishes stronger ties in the UK such as employment and housing. The AV visa is probably the next best thing to ILR in any case. Where such ties are established his/her South African nationality should be less of an issue although I appreciate you can't jump for that 'Alicante for 99 quid leaving tonight deal youv'e just seen on Teletext'. I would recommend a trip to Cape Town to cheer you both up

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Good Luck