How to make Opportunity and Quote Sync work when Quote creation and Opportunity update in made using Process Builder/Flows

Cause:

When Quote is created it is in unsync state and hence the Opportunity.SyncedQuoteId should be null.
 

In this case, when Opportunity Insert, Quote Insert, and Opportunity Update happen in Single Transaction, the flow action sets Opportunity.SyncedQuoteId to the created Quote Id and hence the process detects no change in the Quote Id while syncing and hence does not sync.
 

The Opportunity is saved in a parent transaction and the same transaction is not ended. In the same transaction, the Quote is inserted and the Opportunity is updated. The issue here is the Opportunity entity Insertion and the Opportunity entity save with updated SyncedQuoteId are in the same transaction. Since it is a recursive save, the sync is not triggered during the update action. The Quote Id is anyways updated on the opportunity. 
 

During the start sync process, the quote Id should be different from the SyncedQuoteId field. If it is different, the quote is synced else it is ignored.
 

If a new quote is created manually and synced, synced Quote Id differs from this and hence the sync is completed successfully.
 

As per the Document Flows in Transactions 
Flow's transaction ends when a pause element is executed.

The solution is to separate the transaction.

Create a Schedule Action as "after 0 hours of CreatedDate" in the Process Builder before calling the flow to separate the transaction.

How Does Salesforce Process Scheduled Actions?