Looks like it's caused by JDK-8038734. During deployment registration process, we need to use deploy.jar for the following actions:
-setSecurityLevel
-getSecurityLevel
-getUserWebJavaStatus
-getUserPreviousDecisionsExist
-clearUserPreviousDecisions
-resetUserPreviousDecisionsDate
and when adding new deployment property.

Also, we verify plugin home dir by checking that plugin.jar exists in the directory. Probably, there are more functions that require these .jar files (deploy.jar, plugin.jar, javaws.jar) during installation process.
Currently I have 2 bugs that are caused by this ussue: JDK-8046923 and JDK-8041333, you can find details in the comments. I suppose there are more such bugs, so I guess we still need to copy the .jar files before calling RegisterDeployEx().

Affected cases:
MSI/MSI008-005-M
MSI/MSI008-005-M-64
MSI/MSI008-005-H
MSI/MSI008-005-H-64
MSI/MSI008-005-VH
MSI/MSI008-005-VH-64
MSI/MSI008-007-Lowest
MSI/MSI008-007-Lowest-64
MSI/MSI008-007-Highest
MSI/MSI008-007-Highest-64
MSI/MSI008-008-Lowest
MSI/MSI008-008-Lowest-64
MSI/MSI008-008-Highest
MSI/MSI008-008-Highest-64
MSI/MSI008-009-001-Enable
MSI/MSI008-011-001-Lowest
MSI/MSI008-011-001-Lowest-64
MSI/MSI008-011-001-Highest
MSI/MSI008-011-001-Highest-64
MSI/MSI008-011-002-Lowest
MSI/MSI008-011-002-Lowest-64
MSI/MSI008-011-002-Highest
MSI/MSI008-011-002-Highest-64
MSI/MSI008-012-Lowest
MSI/MSI008-012-Lowest-64
MSI/MSI008-012-Highest
MSI/MSI008-012-Highest-64
MSI/MSI009-001-Enable
MSI/MSI009-001-Enable-64
MSI/MSI009-001-Disable
MSI/MSI009-001-Disable-64
MSI/MSI009-002-Enable
MSI/MSI009-002-Enable-64
MSI/MSI009-002-Disable
MSI/MSI009-002-Disable-64
MSI/MSI009-003-qn-Enable
MSI/MSI009-003-qn-Enable-64
MSI/MSI009-003-qn-Disable
MSI/MSI009-003-qn-Disable-64
MSI/MSI017-003
MSI/MSI017-003-64
MSI/MSI007-002-FF
MSI/MSI007-002-IE
MSI/MSI007-004-FF
MSI/MSI007-004-IE
MSI/MSI007-002-IE-64
MSI/MSI007-004-IE-64
MSI/MSI008-009-001-Disable-64
MSI/MSI008-009-001-Enable-64
MSI/MSI008-009-002-Disable-64
MSI/MSI008-009-002-Enable-64