One possibility is the Sox wanted Bogaerts, just not as a a shortstop. This is basically what they also did with Devers, per every report.
If Bogaerts was not open to changing positions, that means the Sox had 3 options:
1. Give in and let him play SS (or at least tell him he will and force him to change later)
2. Walk away
3. Change the years of the deal (since presumably the money would already align with his new position).