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Ok finally was able to reproduce it, and isolate. It also required patching Hibernate ORM and swap it in a custom build of WildFly.

ClassLoaderHelper.classForName( TIKA_BRIDGE_NAME, serviceManager );

01:29:51,942 TRACE [org.jboss.modules] Finding class org.hibernate.search.bridge.builtin.TikaBridge from Module "deployment.SongUploaderWarArchiveWithTikaIT.war:main" from Service Module Loader
01:29:51,945 TRACE [org.jboss.modules] Finding local class org.hibernate.search.bridge.builtin.TikaBridge from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,949 TRACE [org.jboss.modules] Loading class org.hibernate.search.bridge.builtin.TikaBridge locally from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,953 TRACE [org.jboss.modules] Attempting to define class org.hibernate.search.bridge.builtin.TikaBridge in Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,958 TRACE [org.jboss.modules] Defined class org.hibernate.search.bridge.builtin.TikaBridge in Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,962 TRACE [org.jboss.modules] Finding class org.hibernate.search.bridge.TikaParseContextProvider from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,965 TRACE [org.jboss.modules] Finding local class org.hibernate.search.bridge.TikaParseContextProvider from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,968 TRACE [org.jboss.modules] Loading class org.hibernate.search.bridge.TikaParseContextProvider locally from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,972 TRACE [org.jboss.modules] Attempting to define class org.hibernate.search.bridge.TikaParseContextProvider in Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,976 TRACE [org.jboss.modules] Defined class org.hibernate.search.bridge.TikaParseContextProvider in Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,986 TRACE [org.jboss.modules] Finding class org.xml.sax.ContentHandler from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,990 TRACE [org.jboss.modules] Finding class org.apache.tika.parser.Parser from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))
01:29:51,993 TRACE [org.jboss.modules] Class org.apache.tika.parser.Parser not found from Module "org.hibernate.search.engine:5.3.1-SNAPSHOT" from local module loader @706a04ae (finder: local module finder @6eceb130 (roots: wildfly-9.0.0.CR3-SNAPSHOT/modules,wildfly-9.0.0.CR3-SNAPSHOT/modules/system/layers/base))

Our classloading strategy is able to load the extensions from the user WAR, but while the org.hibernate.search.bridge.builtin.TikaBridge class is found in the composite org.hibernate.search.cfg.impl.DelegatingClassLoaderService - which includes both our modules and the user extension points - it's then identified as found within the hibernate-search-engine module; when this happens, the Class definition is declared as "found" but bound to the hibernate-search-engine module's classloader, and no longer to the composite classloader.
In a second step, the class definition needs to be initialized within its associated classloader (the hibernate-search-engine module), but dependencies to org.apache.tika.parser.Parser and similar (imported by TikaBridge) have it fail.

Looks like a possible workaround is to override the TCCL with a fully composite classloader before initializing TikaBridge, however this is horrible, a better solution would be to extract the TikaBridge and its dependencies in a custom module - so that the user could include this jar as an extension within its own appllication, together with the Tika dependencies. And alternative would be to bundle all necessary Tika dependencies.