One thing you need to be aware of is the M6 cannot select everything. I do not know enough of the technical stuff to explain why, but when you resize with M6, you are only making the model look larger or smaller. There is something that M6 can't edit that tells the game how big the ship is, so even after you resize it, the game still thinks it's the same size. That isn't a problem if you are only making small changes, but it would be a serious problem if you, say, tried to make a K'vort out of a B'rel. In game, the shields will not be correct, for they will be in proportion to the original size. If you make a sphere much larger, the shields will be swallowed up by the model and will not be visible. Also, at a distance the game will resize the ship back to what it's supposed to be, so as you approach the planet, it will at first look small (or large, as the case may be) and then when you get within a certain distance it will pop out to the edited size. I have never used M6 on the planet model, so I have no idea what this would do to the collision feature. It may be that you would be able to fly "into" the planet a bit before hitting it and blowing up, or it may cause some bigger problem. As prone as OP and EAW are to crashes, this might do something wierd.
Milkshape is better for resizing. It has a free trial period and only costs $25 to register, or at least it did about a year ago.