In this world of aggregators/companies/financial institutions that don't have any standards for doing this and no transparency, I can't say anything for sure, only guess. The only protocol that Quicken uses that is transparent is Direct Connect/OFX. Here are some of its attributes.
With Express Web Connect, here is what is published.
To me the bottom line is this. With Direct Connect, you need to ensure that your machine isn't hacked. It would be very nice if OAuth2 was used, but Quicken can't impose that on the financial institutions. With Express Web Connect, it varies with the financial institution, and unless you can get the financial institution to tell you the process they use or guess it from what you have to do to connect to them, there is no telling exactly what they are doing. Getting the username/password out of the aggregator is a good step, but it isn't really that secure unless you have rotating tokens. And note that this is more about the aggregators than Direct Connect/OFX. Charles Schwab stated that then have 4 plus aggregators wanting to get at transactions. They lumped Quicken into that, but it is quite different. With the others the username/password were being stored on the aggregator's servers, but with Quicken they are stored on your machine. So, by changing over to their own API for the connection to Intuit, they have forced Quicken to use Express Web Connect/Intuit/an aggregator. Clearly for the other connections/aggregator storing a "token" is more secure than storing the usernames and passwords of the financial institution, but it is very debatable for the case of dropping Direct Connect/OFX.