On my system the gridlines are aligned. The Ticks are gone already in the documentation on PlotLayout. The purpose for this omission is mysterious to me. Also, some plot in the documentation change their visible Ticks if freshly evaluated in version 15.0, but the plots stay the same when using version 14.1. There may have been undocumented internal changes some time ago.
As for the PlotRange problem, GraphicsColumn could be a workaround:
GraphicsColumn[{Plot[Sin[x], {x, 0, 6 Pi},
GridLines -> Automatic, PlotRange -> All,
PlotRangePadding -> Scaled[.07]],
Plot[100 Cos[x], {x, 0, 6 Pi},
GridLines -> Automatic, PlotRange -> All,
PlotRangePadding -> Scaled[.07]]}]
Thank you. I should have posted that I am on MMA 15.0.1 Win64 on an HP ZBook Fury 16 with an NVidea GPU. Apparently there is some difference in my system or settings that causes gridlines to sometimes be misaligned for me but not for others. I tried forcing MMA to use built in rather than NVidea graphics, but that had no effect.
However, your suggestion of GraphicsColumn does work. I tried it earlier and got misaligned gridlines, but using PlotRangePadding as you did fixed that.
I seem to remember a heated discussion on graphics alignments in the LiveCEOing series. We should expect big improvements in versions to come.
The gridline problem was solved by resetting Wolfram to its default configuration following these instructions
Thank you tech support.