I've never tried this sort of thing but I have done a fair bit of renovating now and have found that the further you can strip anything back the better. i.e. filling and packing and sanding etc. takes a lot of time and effort, you need to come up with a way to get the base correct before laying anything on top if possible.
It is acceptable to sand yellow tongue but not 10-15mm.
Could you rip up the masonite and add packers along the top of each joist to get them flat before laying the flooring?
When you lay yellow tongue on a normal joist floor you are meant to put a bead of construction adhesive along all the joists first. This helps keep it attached but also takes up any gaps under the chipboard ... I think you should consider that too. Get a box of 20 tubes and don't be stingy!! Good luck.