This is by design. There are two different Notes mail contact field holding the assistant value. For the first Assistant under Email section, UserA, is mapped to "work1email" while the second Assistant field under other information, UserB, is mapped to field "Assistant". MNE automatically maps Notes "Assistant" field to Exchange MAPI field PR_ASSISTANT, or PR_ASSISTANT_A and it is reflected in the Outlook Contact.
Because there is one Exchange contact field that logically is used to map the source Notes Assistant field, in order for the other assistant information (as "Work1Email" field) to be migrated, the following scenario guide should be followed:
https://support.quest.com/technical-documents/migrator-for-notes-to-exchange/4.13/scenarios-guide/migration-to-microsofts-office-365/pre-migration-preparations/step-4-install-and-configure-mne/prepare-customattrs-tsv-file-to-migrate-notes-custom-attributes
Please ensure that the SourceProperty column is specified as "work1email" and the value is be picked up and mapped to whatever specified for the target property in the customattr.tsv file.