Putting a bolt through a thin kite line REALLY does not sound like a good idea.
You will be causing all sorts of problems with the line spread open like that.
The reason that a line might become weak is because of how tight the angle is when it bends. This is why if you knot dyneema it loses about 50% of it's strength but it is ok to use a lark's head, which is of course how we attach our lines, as the lark's head has much lower angle than an overhand knot has. When you have an overhand knot in the line the sharpness of the angle causes the line to heat up when it is pulled, and it can reach over 200 degree at which point dyneema loses it's long molecular bonds and that's when a line will fail. There is nothing special intrinsically about putting a bolt through a line that makes it dangerous. I'm not suggesting a 1 pound eye bolt that you use for structural support on a bridge rather a very small few gram bolt with a 2 mm line that is just barely big enough for the line to go through. Maybe you know of some specific problems using bolt that I haven't though of? Now normally I would suggest a spliced line which can than support the full weight limit of the line if you are doing some structural modification of the line. If you use a spliced line then you can hold something like 600-800 pounds from the spliced line. But in the high of a high Y you only have 2 or 3 pounds of force on the bolt itself, just enough to keep the two lines from separating, so there's no real downward or upwind pressure on the bolt as the line just flows through the line freely when it flags and when it's not flagged you just need enough pressure to pinch the lines together.
If you use a spliced loop make a lark's head to loop around the shaft of the bolt your only problem might be the thread eating into the line, or the line slipping off.
Of course your have something machined with a nice smooth groove to fit the rope, but that would be complicated and go against the idea of simplicity.
That said, having to make two splices in the rope is already not that easy to do if you're unfamiliar with splicing.
However, just taking a normal bolt and forcing it through the line (after making it loose) is a terrible idea.
The loading will be very uneven on the individual strands around the bolt, which WILL weaken the line.
Also, the thread is going to chew through the line twice as fast as with a lark's head.
There is probably a good reason why you don't often see bolts jammed into a rope on a professional job.
many depower lines are attached to the cleat with bolt that go thru the center of the line. if you have above the bar depower I would venture to say must do it this way. of course those lines are over spec so it doesn't matter if they weaken but this method is used frequently on the chicken line
As far as I can see the main thing to be aware of when flying a kite designed for a high Y on a low V is that the front line lengths may need to be adjusted. At the kite end for one kite in low V quiver, otherwise on the front lines.
Just loop a small stainless steel ring onto the non flag line and run the flag line through the ring.
Added pic but I did not have flying line or small stainless steel ring handy but you get the idea...
I've tried this ring idea before, and have also seen it suggested before but the truth is that lark's head loosens and it will move all over the place. So I don't like it. I like my suggestion of a small bolt above, but it was criticized above and it's true that it's possible a bolt might weaken the line I dunno, it's worth a try. In the past I have just made a small splice and attached the ring on the splice. Right now I have only V bars no Y bars but if I were to make one right now I would use a tiny bolt and see what happens. Worst that happens is you snap a line and have to swim in. try the ring idea! maybe it will stick in place for you, but it never worked for me.