It's not an artificial limitation. X13DAI is standard EATX and with the increased size of the socket and routing requirements of PCI-e 4.0 they can only fit a limited number of lanes. SP2C741D16X is an enormous EEB motherboard hence its increased connectivity, but EEB is a miserable form factor to work with - the mounting holes don't match any of the (E)ATX standards so outside of a few cases you're stuck drilling your own holes.
sorry, probably off-topic, will try to cut this short and won't expand to any other replies.
I wasn't necessarily talking about PCIe slots (even though X13DAI could have all implemented as X16 instead of having one X8).
It would be great to see at least an effort of delivering these lines via other alternatives (.e.g. MCIO/OCuLink/SFF-86xx or even having an extra M.2, not necessarily M-keyed but E-key for say WiFi or even B-keyed for other devices {e.g. LTE modem} would do too since it's workstation MB and there is plenty of room available on MB surface). Some time ago SM was actively sending a commitment message of implementing all functionality, now this is over.
I was eyeing X12DPG (before deciding to go with Sapphire Rapids in the end, partially because of DDR5 although it doesn't bring much of improvement but at least can be reused on future generations of platforms too, while it's dead-end for RDIMM DDR4, so decided not to waste money on it) and found several affordable cases available on ebay to fit this larger form-factor without much of an effort (e.g. ThermalTake, Phanteks, Antec, LianLi,.., I think some rare models of CoolerMaster, Corsair, PC Specialist, InWin, Abkoncore do have sufficient space too but I had suitable options with first four therefore didn't go into more measurements with latter).
As for drilling case holes - again, with lots of SuperMicro it was always ongoing issue, I tend to have a bunch of 6.5mm hex standoffs/pillars and M3 (prefer metric) relevant tap drill bit ready for almost every of recent builds, shouldn't be a case for whoever does this as occupation or generic consumers of course but for a higher-end system enthusiast having frequent upgrades it's probably inevitable.