The problem was that one if the the serialized string lengths did not match its true string length. One of the migration steps was to change the domain name in the database SQL file with:
sed -i 's/old-domain-name/new-domain/g' db-dump.sql
One of the theme mods was a string that contained the old domain name. When it was changed to the new domain name, the length of the string was not adjusted to to match the new string length. Therefore, WordPress was unable to properly read the theme mods.
Lesson: Be careful when doing a global find and replace on the db-dump.sql file!
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