MeOH has other chromatographic properties other than ~10% less solvent strength. It can also have an effect on peak selectivity. If you just tried to adjust the %B, you may end up altering the peak elution order. I have an example of a glimepiride impurty method where the elution order for acetonitrile is A,C,F,D,E,B and for MeOH is A,C,D,B,F,E. Same method, same column, same pH, same temperature.[/img]
I certainly did not mean to insinuate that methanol could always be substituted for ACN. Instances such as you have mentioned with multiple components would be such a case. However, I developed and validated a method recently where prior to validation I evaluated MEOH vs ACN, 50 mm vs 100 C18 column and flow 0.2 or .25 mL/min. I settled in using a 100 mm column and a methanol mobile phase but the method would easily have run successfully with either.
Tell me, in your example, do you think that elution order of components would match that of ACN if you used a methanol mobile phase adjusted to the same solvent strength with IPA and/or THF?