I wouldn’t be put off the high route by the cleat – ours is on the aft face of the thwart at an angle, but the wire lead at the ‘back’ of the cleat deals with the change of direction quite well, to the cheek block under the thwart near the cb case. Then it’s more or less straight route forward to the tabernacle.
However, if the floorboards are really well secured in place and the new block won’t interfere with sailing/sleeping etc then through-bolting with some kind of backer will probably be fine, I would think. A good opportunity to overhaul your ‘boards and their fixing method.