Pep coached Thiago for 8 consecutive years at Barca and Bayern, brought him to Munich and immediately tried in a pivot role. It was a disaster, he's not positionally disciplined enough to play there. Used him as 8 after the initial fiasco. Thiago spent a lot of time on the bench in Pep's 3rd season at Bayern.
Thiago Alkantara isn't worldclass, not consistent enough. Besides, he had 2 consecutive ACL injuries and lots of lesser health problems. Doubt that Bayern supporters would be devastated to see him leaving.
In terms of playing in DM position Jorginho and Thiago are on a different level. Lots of sceptical posters will call Jorginho 'worldclass' in a year if he signs.