Stefaan/Franek
It has taken me a little while to find a document in my files. In among some MAAF papers at the National Archives/PRO I have found an odd, isolated, very brief "Loose Minute" (there were no other documents around it that linked to the same issue). It reads simply:
TO: WAR ORG
SILVER SPITFIRES
The unpainted Spitfire IXs which are being prepared may be sent as normal replacements to any T.A.F. Spitfire Wings except those in Corsica.
Wing Commander
Combat Operations
21st May 1944
Clearly this is not much more help whether your first language is Afrikaans or Polish it is not totally clear in English!

The note seems to confirm that the command system knew that NMF Spitfires existed and did not regard this as a problem. The words "which are being prepared" could mean that the a/c were stripped in the Med rather than delivered unpainted.
In the excellent book "Spitfires in SAAF Service" by Steve McLaren there are several photos of NMF Spitfires which are ALL referred to as Special HF MkIXs. Are those the photos that Stefaan refers to?
I believe there was quite a lot of experimentation in the ME with suitable colour schemes for high flying Spitfires. Is it possible that the paint was stripped because the colours in which a/c were delivered were thought unsuitable of high altitude work? In saying this I realise that NMF finish is unlikely to be a suitable replacement "camouflage".
Every little bit helps (sometimes)
Steve