Hi, welcome to the LAF

As it is, I tend to put my 28mm minis in the foam all lying down. Reason for this is the fact that a lot of minis have fragile elements sticking up, like rifle barrels, spears or pikes, waving hands, etc. And when stacking foam trays on top of each other in a carrying solution, especially with metal minis, the weight will compress the foam trays, potentially snagging or breaking any protruding thin miniature parts, not to mention impacts like setting the bag/case down or *gasp* dropping it.
And when lying them down, your tray can be a lot shallower, meaning easier access to the miniatures in question. Also; my first case was a GW one, and the red foam in there was geared towards lying down miniatures.
There are probably arguments against transporting them lying down too. The most obvious one being wear and tear on the paint job by the (ever so slight) abrasive qualities of the foam. But that's nothing a good coat of varnish couldn't prevent I'd say.
In fact, I'm usually quite the slacker when it comes to varnishing my miniatures; I'm usually too happy they're done, and straight into a photo shoot and then the display cabinet they then go. And from there, it's often straight into the foam for a battle, and I've not experienced any negative effects on my paint jobs from the foam so far, in decades of operating like that.
Another negative could be space; a cavalry miniature will take up a lot more surface lying down, than standing up. But obviously, the space you lose like that is compensated for by a reduced height of the tray. So probably both solutions would result in the same cubic space being occupied (but I'm sure some mathematician could prove me wrong here

).
In the end; I think most products offered will be geared towards lying down your 28mm miniatures, and upright placing of multi based, smaller scale miniatures, probably because of the convenience offered by either solution for the respective scales...