Historically yes but then again historically most teams have struggled against the Windies. Also Australia only became ATG in 2000s. In 90s they have also lost in SL, in Pak, drawn in WI etc. Only post 99 WC they actually became the behemoth they were.
Thing is post that series (which was just post match fixing) when India actually become a good side SA have lost two series in India (0-1,0-3) and drawn two (1-1,1-1). India have lost three (1-2,0-1,0-2*) and drawn one (1-1). Both sides are at 2-6 in each other's conditions since then.
I am not arguing against the fact that SA has been better than India historically in each other's conditions, just laying credence to Virat's statement about South Africa not really performing well in India. Dredging up matches with the likes of Donald, Rhodes, Kirsten etc who have retired long ago has no place in this argument.
Ah, I love selective stats dredging to prove some sort of point.
But as it happens, you are wrong. You missed out on the 2001/02 series which SA won 1-0. And even that underestimates South Africa's superiority because it should have been 2-0, but India threw an almighty temper tantrum and the third test did not have test status (A taste of things to come from the BCCI)
So, even if we start by your preference of beginning the count after arbitrarily (and conveniently) leaving out the series where SA comprehensively won in India, they are still ahead during that time frame. In that time they have won
4 series at home (1-0, 2-1, 1-0, 2-0*) and drawn only once (1-1) with an overall record of 7-2 (Should actually be 8-2 remember, and with the whitewash still to come to make it 9-2 potentially). India in contrast have won only
2 series at home (1-0, 3-0) and drawn twice (Both 1-1) with an overall record of 6-2. Four series wins at home and two draws away seem to be superior to two wins at home and only one draw away. Even India's 6-2 record is misleading because it rests on the last (3-0) series with absolutely unprepared bunsens, rated poor by the ICC, and where Dean Elgar became a genuine wicket taking threat. Before that SA were always competitive in India. And contrast those pitches with the India-friendly flat ones gifted by CSA this time in Centurion (And in Johannesburg and Durban in 2013/14) where India still can't win and the contrast becomes even more glaring.
Arbitrarily pick and choose to find a stretch of series's where it looks like India in SA are the equivalent of SA in India all you like, but it does not change the facts. India have never been and currently are not, as good or competitive in South Africa, as South Africa have been in India. Rant over!