Sighting through the bore to the line is doing nothing but adding a step that doesn't matter. You have no means by which to ensure it is passing straight between 12:00-06:00 other than "eyeballing it".
Eyeballing the plumb line through the bore is not a perfect method, but IMO it is quite accurate if you are careful about it. Kinda like reading a level... that is also "eyeballing". Being a construction contractor, I have quite a bit of experience with plumb lines, bubble levels and laser levels. If you accurately align your bore and reticle to the plumb line you most definitely are ensuring that your reiticle is aligned (pointed to) the bore.
If your receiver is milled so poorly you are going to have an issue leveling off of the top of it, I can't see how you can correct such an error by leveling through the bolt raceway.
Either your receiver is milled perfectly or it isn't. If it's not, then using it as a reference will induce error. Once again, any error in the receiver machining, hole drilling, rail machining and holes and contact irregularities between the rail and receiver and error of setting the bubble tube itself in the rail will induce errors to what you read on that in-rail level.
That rail level is nothing more than a placebo. There's a chance it could be accurate but there's a greater chance it isn't. To "assume" that is accurate is to assume that...
The receiver is machined and drilled precisely and accurately.
The rail is machined and drilled precisely.
The torqued contact between rail and receiver is precise.
The bubble tube is set precisely in the rail.
That's a lot to assume.
All you are doing essentially here is eye balling the bore alignment to ensure that both the scope and bore are aligned similarly left to right.
I am using the a straight and plumb line as reference to align the scope to the bore and then mount and accurate level in reference to no kidding gravity.
If the top of your receiver is off, then you will not get proper squaring no matter where you choose to set your level, but, if you use a level on the top of the receiver/rail and align your vertical crosshair with it, you will be square and level.
The top of the receiver becomes the cross of an upside down T when you mount the scope. If it is milled with a left to right can't to it, no matter what you do above or below it you will still be slightly off center because the leg of the T is essentially your vertical cross hair which is then leaning left or right.
Wrong. You can properly align your scope to your bore, them mount a level to ensure everything is aligned and tracking according to the pull of gravity. If your receiver is off, then it will be canted to properly align the scope to bore to gravity. Drawings can show this very easily. You can see an extreme example of it in the picture of a rifle that David Tubs set up. I will attach in the next post.
No matter what, it is then out of center to the bore. You will know this as soon as you mount the rail because the rail will twist as you torque it down.
If you are using your raceway to level from you will also know instantly whether or not the top of your receiver is out of square when you level the rail anyhow.
Using the raceway to level from is assuming the race way is square to the mounted scope.
If it's out of square enough to matter you are already screwed because as I said above unless you shim it to square it your scope will never be centered exactly above the bore no matter what type of mounting system you are using.
See the picture below