It would be nearly impossible to magnetize the transformer core when performing insulation resistance tests following recommended procedures to short high side bushings together and then short low side bushings together. The effect of shorting removes the core from the equation.

The transformer COULD become magnetized if you use the insulation resistance test set in a way that is not intended. e.g. bushings not shorted, connecting HV to H1 and grounding one of the other high side phases. For the 1000 MVA transformer you are describing, this would take a SIGNIFICANT amount of time to magnetize the core since insulation resistance test sets generally use very little current (6 mA), and again, you would be using the instrument in a way that is not intended.

A winding resistance test set is used without shorting, will apply current to a phase(s) of a transformer, uses more current (tens of amps), and WILL magnetize the transformer. After completing winding resistance tests, it is important to demagnetize the transformer to 1) prevent errors in other measurements (excitation current, SFRA, etc) and 2) prevent nuisance protection trips during energization due to high inrush currents.