Years ago, I had a talk with a pro & lure designer & asked him about the flat vs inline jig eye thing. He told me the "flat eye advantage" was bunk & simply marketing strategy to get people to buy from the large manuf. who had access to flat eye hooks instead of the small jobbers who had only the inline eye hooks to use. He also claimed that jighead design (shape, line tie placement, overall balance etc) was 1000x more important than the line tie orientation regarding how well a jig fished & caught fish. Seems to make sense as the head is much larger than the line tie & should be the main influence as a jig comes through cover.
I do know that with an inline eye, you can cinch a palomar knot down on the bottom of the eye so the line points to the bottom of the head, you can tighten up & release line pressure to make a jig rock back & forth in place, and weeds dont get wrapped around the eye as easily.