...has the default value of yes, as noted at http://docs.basex.org/wiki/Serialization, the XQuery Serialization does not appear to recommend/enforce a default (http://www.w3.org/TR/xslt-xquery-serialization-30/#XML_OMIT-XML-DECLARATION), but the XForms spec does (http://www.w3.org/TR/xforms11/#submit) and the recommendation in XForms spec is the default value of false (=no), which is different from the default value of yes(=true) used by BaseX.
We decided to omit the xml declaration in BaseX by default, as we observed it's the preferred choice by many users (esp. if XQuery is used to produce results other than XML nodes). An alternative default setting could be used for JAX-RX, but this would currently be the only exception in the existing framework.
...and it would be nice if BaseX/Jax-rx allowed true and false to be used in addition to yes and no (wherever it currently allows yes and no as the values)
We'll think about that (I frequently mix up the allowed values by myself; however, an extension to "true" and "false" would conflict with the specs and, thus, might break some tests).
Thanks for your suggestions, Christian