This is not true, there's no conflict. The Buddha was not interested in abstract doctrines but only in what was most pragmatically useful for attaining stream entry, enlightenment and liberation from craving and desire. People who are actually pursuing these goals, even in modern times (with very compelling results, though obviously any claims to arhat status will always be viewed skeptically by most) have clarified how anatta is entirely compatible with a Higher Self as with Brahman.
https://en.wikipedia.org/wiki/Adi_Shankara
From the second para:
He also explained the key difference between Hinduism and Buddhism, stating that Hinduism asserts "Ātman (Soul, Self) exists", while Buddhism asserts that there is "no Soul, no Self".
For that matter, even Shankara's description of the Atman is entirely in the negative, stating what the Atman is not. So even while accepting the existence of the Atman, he's clearly tending towards a universalist description that, again, is quite compatible with a practical understanding of the Buddhist doctrine of not-Atman.
Buddhists themselves reduced the historical Shakyamuni to one member of a pantheon long ago. This was a clear trend in Mahayana and Vajrayana before Allauddin Khilji came and settled the issue once and for all.
It is troubling to see how the current wave of jingoism coupled with religious fervor is trying to reduce the Buddha to a mere pawn in an imaginary, all-encompassing Hindu pantheon. Maybe you are not deliberately trying to do this, but the muddled and confused efforts of numerous foot-soldiers expose the sad trend all the same.