I was mistaken that you were referring to amending the 2018 return since you kept referring to the return her former accountant prepared.  That's also why I referred to 5.1% instead of 5.05%.

The filing instructions may not be very explicit about what to include in the denominator but Chapter 62, Section 3 is. 

Part B paragraph (b)(1)(A) permits only $4,400 for MFS taxpayers.  Paragraph (c) then stipulates that the denominator of the ratio "is the amount which would have been his Massachusetts gross income had he been a resident of the commonwealth throughout the full taxable year." 

Similarly, 830 CMR 62.5A.1(7)(b) explains that "[t]he total exemption amount must be pro-rated by the "deduction and exemption ratio" of the taxpayer's Massachusetts source income to his or her total income."

The law does not provide for any special adjustment for the other spouse's income in relation to this proration.  And this would make sense because no personal exemption is allowed for the other spouse.  In other words, she is correct that her husband's income does not need to be included in the denominator.

I think it's the instructions for Lines a and b that were confusing but if you read them carefully, the instructions to include the other spouse's income is applicable "when completing this section" only.  The verbiage about including the other spouse's income does not appear anywhere else.

For example, if she had only $22k in MA wages but no other MA-source income but her total income on an as-if resident basis was $55k, the ratio will be 0.40.  If she is eligible to claim two dependents and the total exemption is $6,400, the prorated exemption that could be used to offset her 5.05% income would be $2,560 ($6,400 x 22/55).