No one seemed interested, however I found a solution and will answer to my own question.
Apparently, assignment of an Excel Array Formula within C# code works only if the formula is in A1 style, not in R1C1 style. In my case, I was starting with a R1C1-style formula, so it required conversion to A1 style. This is achieved by assigning the original R1C1-style formula to the top left cell of the target range:
topLeftCell.Formula = myR1C1Formula;
// topLeftCell.FormulaR1C1 = myR1C1Formula also works
Assignment to that particular cell will ensure that A1-style formula contains correct references. Get back the converted formula as a string:
string formulaA1 = topLeftCell.Formula;
Get reference to the whole target range by rezising the top left cell:
Excel.Range newArrayRange = topLeftCell.Resize[height, width];
Resize operation must precede the following assignment. Finally, assign the A1-style formula to the FormulaArray property of the whole target range:
newArrayRange.FormulaArray = formulaA1;
This works perfectly without issues or side-effects.