Do you have an HVAC guy you trust? Without seeing the layout or knowing what your renovations would be, I feel like you can perhaps have your cake and eat it too.
If the footprint of the house isn't likely going to change with your renovations there should be no problem with the replacement of the furnace unit itself. If the footprint changes, then you might have issues with capacity and where the "lines" (vents/pipes/returns) are run. The line location is a renovation problem not a furnace problem, unless there is a chance you will move the furnace too (or need a second unit). But even then, if you already feel you have a capacity problem (because of that current room not getting enough heat/air) you may have a capacity problem anyway, and so whatever upgrade you do now can, with a little foresight, cover your renovation plans.
A reputable HVAC person ought to be able to meet with you for half an hour and give you reasonable advice. I know for me, unless my renovation plans were WILDLY variable, I wouldn't let the future renovation drive my decision to REPLACE the furnace, only what I replace it with. Does that make sense?