The phrase "almost certainly referring" is correct and usable in written English.
It can be used when you want to indicate a high level of confidence that something is being referenced or alluded to, but without absolute certainty.
Example: "The author is almost certainly referring to the historical events of the 18th century in this passage."
Alternatives: "likely alluding to" or "probably referencing".
Miller was almost certainly referring to what he perceived to be dirty play by Fox.
"I have often read the sentence – they are God's poor," she had written to Post, almost certainly referring to a line in William Andrew Smith's 1856 proslavery lecture "The Duty of Masters to Slaves": "They are God's poor, committed to us.
If we were two Lego blocks even the Harvard University graduating class of 2010 couldn't put us back together again" (Which, now I think of it, was almost certainly referring to that White Stripes video and the tedious over-intellectualised-noodling that surrounded the band at that time. Possibly).
Van Gaal talked afterwards about the new arrivals being too eager to impress and he was almost certainly referring to Morgan Schneiderlin, at the base of their midfield, and Depay, who was operating just behind Wayne Rooney but might be better on the wing.
That ten hour battery life claim is almost certainly referring to a six-cell setup.
And he was almost certainly referring to Ferrari's decision to trigger a gearbox penalty for Felipe Massa to move Alonso up a spot and on to the clean side of the grid in Austin.
This almost certainly refers — by way of Gematria, the Jewish numerological system — to the contemporary Emperor Nero.
Deccan almost certainly refers to the Deccan Plateau located in the South of India, an area that is becoming a hot spot for militant recruitment and operation.
Although the report does not identify the country that manufactured and delivered the weapons, Pentagon analysts say the missile proliferation statistics almost certainly refer to North Korea.
Big Peaceful Water, Big Pond and Snake Lake are among the various translations of a word that almost certainly refers to the 593-acre body of water that distinguishes the hamlets: Lake Mahopac.
In fact, the signs almost certainly referred to sugar-beet; even so, to equate "betteraves" with those other non-edible road-threats such as "gravillons," "chutes de pierres" and "chaussée déformée" seemed a little contemptuous.
