Can the Office 365 E3 Plan be upgraded to Office 365 E4 as part of the Enterprise Cloud Suite?

Yes, this is possible. By default, Enterprise Cloud Suite includes the Office 365 E3 Plan. In addition to it , the Office 365 E4 Plan can be obtained as an Add-on User Subscription License.

Source: Flyer_Microsoft_Enterprise Cloud Suite 2016-08-24 (German only)