There is a simple reason why the holes are deeper than the threads.
The holes are power tapped...if the tap hits the bottom of the hole, under power, the tap will break. This halts production, and scraps a part. Drilling the hole a little deeper ensures that the tap will not bottom out.
2-1/2 times the diameter is generally accepted as being a good engagement depth for studs in Aluminum.
The 6mm studs are .230" in diameter, so .575" thread depth is good.
I always bottom tap the engine mounting holes and the exhaust stud holes as they are never threaded deep enough. I've never had a problem with the jug assembly studs...I suppose eventually I will...
Whether or not you should replace the studs from new depends on several things.
1) Are they actually studs? Or are they lengths of all-thread that have been cut from stock?
Studs have threaded ends with a length that is not threaded in between. Studs are made on a screw machine using specialized cutters, or roll forming tools. The ends will be clean and chamfered, (beveled). The studs will be a uniform length. All thread is, just as the name implies, threaded the entire length. All thread is manufactured using an entirely different process, and the grade of material used is generally softer to accomodate the manufacture. The all-thread pieces will typically be different lengths, and the ends will appear saw cut with a non uniform bevel...probably sanded by hand, after cutting.
NOTE: Different grades of all-thread are available here in the U.S. My comments on all-thread apply to what comes in the factory kit.
2) Did they get bent during shipping?
Whether your kit came with studs, or all-thread...if they got bent during shipping, throw them out. Do not attempt to straighten them. They are likely already fractured, and for the small amount that hardware costs it's not worth the risk of having to drill out a broken piece.
So...If your kit came with "real" studs, and they are straight...use them.
If your kit came with all-thread, or any of them are bent...replace them.
As far as engine break-in goes...I haven't had any problems running them heavy on the oil initially, (20:1). I run two tanks, or one gallon at 20:1. After that it depends on the oil you are using. I've been using pennzoil for both break-in and there after. After break-in I use 4 ounces per gallon, which is a ratio of 32:1. I haven't had any problems with carbon fouling.
I, too, agree with Joe. I've never had any other 2-cycle engine where a heavier oil mix was recommended during break-in. So, why do I do it...
1) It hasn't hurt anything to run a little heavy on the oil initially.
2) I have yet to throw away an engine.
Jim