There are some features of XSLT 2.0 that can't be invoked directly using JAXP, for example the ability to start execution with a named template, or the ability to use some of the new serialization options. If you want to use such features then you will need to use Saxon extensions of the API, or the new Saxon-specific s9api API introduced in Saxon 9.
But for the most part, JAXP doesn't care what goes on inside the stylesheet. Just because your stylesheet uses xsl:for-each-group doesn't stop you running it using JAXP interfaces, so long as you take care to invoke an XSLT 2.0 processor.
Author, XSLT Programmer's Reference and XPath 2.0 Programmer's Reference