I think it's easy to understand if you think about what holds up the two ends of the bike on the trainer. First off, the bike is level if a line between the two wheel axes is level, but this is hard to measure, compared to a properly-made level top tube.

The rear wheel is held up by the trainer frame, attached to thte bike at the axle. The height above the ground only depends on the design of the trainer and bike frames and whether the trainer is sitting on the floor or perhaps is shimmed or padded. The front wheel is supported at the tire, which rests on the wheel block, homemade or not. So the size of the front tire is a factor. Kurt had some front tire in mind when designing the support block, but I don't think they tell us what tire, pressure, and block position is intended to be level. This is kind of like a calibration condition, that they don't define.

Another variable is that the floor might not be level, or the trainer frame might sink into the carpet farther than does the front block (or vice-versa).

As far as pre-conditions for a level bike, there is a unique pre-condition but we don't know what it is, and there are many variables. I think the real bottom line is to vary the thickness of the front wheel support (i.e. how many old issues of Bicycling! you will put under the block) using a good level (digital, bubble, dial, plumb-based or whatever) some reference point on the bike frame to determine when it is level. My frames have level top tubes (a retro-grouch, yes) so it's easy for me.

For fitting and setup, I like the bike level, so I agree that you should work on this.