Maybe i've misunderstood but...
You can manually spread dirt around to fill holes
hold dirt in hand and right click the ground to fill holes (start at the bottom of the hole or try to reach the sidewall of a hole)
Or do you mean with even more precision ?
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I'd like to see the rake getting a tweak tho (which is the most complained about)
Filling a hole without creative mode never seemed to be a problem for me or anyone i've met online yet.
Yes the wiki has a low priority right now it seems since everything is still subjected to change this early in development.
Glad i could help you out, I wish you great success with your building project!
The problem with using your hand to fill holes is that they get very irregular shapes after that.
That where the rake comes in, so I am finding ...
exactly 
The problem with using your hand to fill holes is that they get very irregular shapes after that.
like real life spreading around dirt manually isn't as perfect as when you smooth it out with a tool (rake).
