There are some diffs and missing features when installing JBT from Marketplace vs installation from JBT. And definitely installation from Marketplace for some features (central) is incomplete
Some of these diffs can be intentional, some of them are definitely missing, like part of Central (missing project examples on central page). I would prefer to have installed the same content as from US.

Steps:
1. Install JBT M5 from Marketpace
2. Install JBT from US (http://download.jboss.org/jbosstools/updates/development/indigo)
3. Check diffs

JBoss BIRT Integration 1.3.0.v20111208-2002-H38-M5
JBoss Central Community 1.0.0.v20111213-1606-H19-M5
JBoss GWT Integration (Experimental) 1.0.2.v20111208-2109-H29-M5
JBoss Tools Common - Mylyn 3.3.0.v20111208-2036-H34-M5
JBoss Tools EGit Integration (Experimental) 2.3.0.v20111213-1457-H21-M5
JBoss Tools Java Standard Tools 3.3.0.v20111208-2115-H35-M5
JBoss Tools JSF 3.3.0.v20111213-1958-H41-M5
JBoss Tools Mobile Browser Simulator 3.3.0.v20111208-2357-H33-M5
JBoss Tools Usage Reporting 1.1.0.v20111208-2055-H31-M5
JBoss Tools Visual Page Editor 3.3.0.v20111208-2357-H33-M5
Struts Tools 3.3.0.v20111207-0022-H37-M5

Complete file list added