Next ORM Designer version will contain following update:
We extended Doctrine2 export scripts to export custom properties for owner/inverse side and for association columns properties. Here is our test case:
Our custom configuration xml:
<struct name="Association">
<attribute name="custom-root" .../>
<struct name="side-owning">
<attribute name="custom-owning"...>
</struct>
<struct name="side-inverse">
<attribute name="custom-inverse"/>
</struct>
</struct>
So our ORM Designer Property editor now looks like this:

If you fill properties like in our example, result doctrine XML will looks like this:
<entity name="E2">
...
<many-to-one field="t1" target-entity="SampleEntity" inversed-by="t2" custom-owning="custom-owning">
<join-columns>
<join-column name="sample_entity_id" referenced-column-name="id" nullable="false" custom-root="custom-root"/>
</join-columns>
</many-to-one>
...
</entity>
<entity name="SampleEntity">
...
<one-to-many field="t2" target-entity="E2" mapped-by="t1" custom-inverse="custom-inverse"/>
...
</entity>
And of course this same is true for YAML export format:
E2:
...
manyToOne:
t1:
...
customOwning: custom-owning
joinColumns:
sample_entity_id:
...
customRoot: custom-root
SampleEntity:
...
oneToMany:
t2:
...
customInverse: custom-inverse
I hope we cover all possible variants. This update will be available in the next ORM Designer release.