To all you 29er's out there!

Say I get a 410mm layback post (as I also feel like the cockpit is quite short, but this may be because I'm used to a road bike and have no MTB experience) - is this going to radically change the bike's handling compared with gaining the extra length in top tube?

Probably not.

You dont want to be too far over your rear wheel, because it can cause problems when climbing. A bit of a set-back on a seatpost should'nt do this though.

Also you do want your bars closer (more under your shoulders) on a mountainbike. As you want to be able to lift/plant the front wheel over obstacles. A higher saddle position will push your shoulders forward slightly. So your new set back + longer saddle should have a lesser effect than you think.