Persisters use a fixed "SELECT" SQL statements

I am currently trying to work with BINARY columns with Doctrine 2 and MSSQL. In order to get my Entities working I had to create a custom Mapping Type for Binary columns. All went well in this case and I've got it running.

The problem arises when I am attempting to use Associative mapping (OneToOne/ManyToMany). The problem is, in order to do a select for an SQL column, I had to create a DQL function called "CONVERT" so that I use WHERE statements:

return $this->createQueryBuilder('u')
->where("u.id = CONVERT('binary', :id, 1)")
->setParameter('id', $id)
->getQuery()
->getSingleResult();

As you see, I must do this in order to get a result.

However, when I'm using associative mapping; this is what it does:

return 'SELECT ' . $this->_getSelectColumnListSQL()
. ' FROM ' . $this->_class->getQuotedTableName($this->_platform) . ' '
. $this->_getSQLTableAlias($this->_class->name)
. $joinSql
. ($conditionSql ? ' WHERE ' . $conditionSql : '')
. $orderBySql
. $lockSql;

As you can see, its some what hard coded and I cannot change it without changing the actual code in
Doctrine\ORM\Persisters\BasicEntityPersister.php

So, I would first like to know if there was maybe a way you could allow us to customize the SELECT statement that the persisters use - or maybe (though I'm not sure how this will be done) make them use user-defined repository functions?

Like $myRepo->find($identifier)

Not entirely sure if I explained this properly and I do realize my circumstance is highly odd - but this does seem like a limitation and because of this I cannot use associative mapping.