I love staking my cake by driving a dowel rod down the middle of stacked cakes. Only thing is, if you're doing a buttercream cake, you can easily patch up the hole it leaves in the top cake...but what about a fondant covered cake? How do you guys patch up the hole?

Royal icing or decorations or topper

Cut a whole in very center of the cardboard of the top tier....stake all the cakes below top tier as usual leaving about 3 1/2" of the dowel above the cakes....put the top cake down on the dowel....no whole in the top frosting!

When using a 'stake' as you describe I always leave the dowel about 3" longer than the cake is tall & remove it once it is in place.
There is always some decoration or icing you can use to cover that hole.

I use drilled masonite board and mount the center dowel to the baseboard and lower the subsequent tiers down onto the center rod. If I have measured correctly, the dowel will only come 1/2 to 2/3 the way into the top tier and there is no hold to have to worry about.

I make my dowel longer than the height of the cake so that it can removed once it's been delivered. For weddings, I simply make two small fondant hearts, stamp them with the couple's initials, and place them over the hole. It's an unexpected touch that couple's love and it doesn't detract at all from the overall look of the cake.