I think the slot layout was done with good intentions;
At the time, a Pentium would have cost anywhere between $2500 and $9000 - not adjusted for inflation, so what would that be in today's money? A heart attack most likely - so given the cost there are only two reasons you would buy a Pentium at that time...
1. You're rich and an idiot, it's 1993/4 and you have to have the best computer. The more expensive system must be better!
2. You are a professional, you need the power and that need outweighs the cost / the cost is no object as your company can afford it and will likely make it back from the output of the system.
Thus, in the latter scenario, we may imagine that the user may need specialist hardware... He may be video editing or something (Used as an example because this is my thing) - so he needs a high-end video card or specialist editing cards. Have you seen the early PCI implementations? Look at the V7 ShowTime Plus with its capture hardware, MPEG decoder and so on... a Pro editing rig would probably have several specialist cards with similar (likely larger and more powerful) hardware onboard as this one, thus they would be similar lengths. Some editing cards and particularly broadcast systems practically had their own entire computer system on the card required for things the main CPU couldn't do yet.
You wouldn't use ISA, because that would be pointless. You bought a 486 if that BUS was adequate. Your Pentium editing rig would maybe use one long audio card, but any other slots would be for LAN (10Mbit ISA), RS-232 or modems. You know, small cards of little importance.
Another possibility is a server where again, you'd use PCI SCSI and not ISA in such an expensive system. High end cards with Cache and CPUs were sometimes very long, some even had multiple SCSI systems one a single card - a few years back I worked on one that had FOUR SCSI controllers on a single card, all together there was more CPU power and RAM than the motherboard it plugged into. Even late high-end SCSI/VHDCI boards were often large.
At least, this is my theory. It is also possible that as everything else on the Batman motherboard is awful the designers just messed up the layout too... I noted the HSF gets in the way on mine.