Hi there,
Apparently this is not how the Process Builder works. The validation seems to be working properly, as there should be a Join Type defined when there are multiple incoming transitions to a route.
But as you say that the Join Type field is not available when the input and output transitions lead to a Process Tool, then I would really call it a bug and would suggest you to reach out to Joget.
In that case, please see if there are any JS errors on the web console for this and confirm what version of Joget are you using as I haven't encountered this in v5.0.11. In the meanwhile, you can use the good old Workflow Designer or add this following section (by replacing your values) in the debug dialog of the Process Builder:
<xpdl:Activity Id="route2" Name="">
<xpdl:Route/>
<xpdl:Performer>participant5</xpdl:Performer>
<xpdl:TransitionRestrictions>
<xpdl:TransitionRestriction>
<xpdl:Join Type="AND">
<xpdl:TransitionRefs>
<xpdl:TransitionRef Id="transition4"/>
<xpdl:TransitionRef Id="transition6"/>
</xpdl:TransitionRefs>
</xpdl:Join>
</xpdl:TransitionRestriction>
</xpdl:TransitionRestrictions>
<xpdl:ExtendedAttributes>
<xpdl:ExtendedAttribute Name="JaWE_GRAPH_PARTICIPANT_ID" Value="participant5"/>
<xpdl:ExtendedAttribute Name="JaWE_GRAPH_OFFSET" Value="966,43"/>
</xpdl:ExtendedAttributes>
</xpdl:Activity>
Hope this helps!