I haven't contacted Lacerte, yet, to get their suggestion. I'm hoping to have time next week.

Pressing F1 on the "Married filing separate and spouse not filing" input checkbox gives this note:

"This checkbox does not automatically exclude the spouse's income. The federal return must be set as Married Filing Jointly with the spouse income already excluded."

My backup plan if I don't get advice from Lacerte is to copy the client and remove the spouse's income and split the rest so MT shows just the taxpayer's earnings and half the investment income and itemized deductions. Then use the first client file to e-file just the US return and the second to e-file just the MT return.