No, not without making them copies.
Se the way freeze transfrom works is it takes the object and takes it local space and zeroes it out in relation to your origo. Its not just a magic button to make objects transforms 0 it affects the entire hirarchy below. (freeze transform isnt something most people would do so lightly if they realy understod what it entitled)
BUT instances SHARE shapes, so the only way they can be at a different position is that their tranforms are different. (because if youd be able to share shape and would let to freeze all isntances would change immidiately eventualy all being at the same powsition, something you most certainly never wanted).
But it can be facilitated with 2 ways. One make extra transforms a group that transforms and then leave the instace at 0 never moving its parent transform. For the users standpoint the effecty is the same if he never bothers to look at the hierarchy.
A second way would be ot device a completely new set of attributes that seemingly house 0 out values then hinding the originals feeding the difference to the actual values with the ofset calculated in (thisway the user woudl never noice its happened altough ts more painfull to set up whitout mel). The downside offcourse would mean NO manipulator tool use wahatsoever, unless you diverted the source to alocator or something.