Small benchtop jointers can have some limitations with long boards.
The leading edge of the infeed table, the apex of the cutter, and the trailing edge of the outfeed table are three points that describe an arc. Especially if you're using a deeper setting, it's possible that in the middle of the board, it is riding on the two ends of the table and slightly lifting off the table near the cutter, still taking a chip but not at full depth, so it will joint a concave radius into the board. It may be many meters in diameter, and when you bring two of them together it shows 1mm over nearly 2m. This would present as your boards being slightly hourglass shaped as you describe. Also, it's possible the tables of a light duty jointer can sag under the weight of a very large board, exacerbating this problem.
Some things that help when using my benchtop jointer:
- Rip the edge on the table saw first to get it straight if saw marked, then take it to the jointer. Using a taper jig as the reference on the fence may help if the board is bowed or otherwise not straight. Your track saw is also a good tool for this.
- Set the jointer for a shallow cut. The shallower the cut, the larger that radius becomes. This can reduce but will not eliminate the issue.
Your thickness planer won't help here, because what it will do is take your hourglass shaped boards and make banana shaped boards. You'll go from )( to )). You might could make that work but it's still a problem. I'm also just not a fan of putting boards through a planer on edge without ganging up several.
Rhe most straightforward solution is probably to use a bench plane. This video from Paul Sellers is a great reference for the method. It's either use a hand plane, get a bigger jointer, or try some hacky workaround like use a router and a straight edge. Maybe you can use one of those power hand planers they make with the same techniques as a bench plane but I honestly don't think those are any easier to deal with than a bench plane.