1. Right, there is no possibility to pass an array of URLs or input streams anymore. In our plans to support a possibility to call readHTML() multiple times: to append new docs to already loaded one(s). Before the feature is implemented, you may just merge multiple HTML docs to a single one and pass it to PD4ML at once.
2. It was not supported in v3. A workaround is the same as in #1: merge HTMLs before the conversion.