To add, the system provides the best protection with a good level of compression, although even at lower levels of compression it still exceeds the protection provided by dumb foam. The flexible polyethylene construction of the vault cases in many instances show case lid bowing even when empty, but in any event, the softer material will likely show some deflection in order to achieve the best levels of protection. The seal stays as closed as it is on the case normally, even with significant deflection. The molding warpage of the case lid itself will show gaps in the overlap--and it does this on the vaults in many cases even when empty--but the seal is still engaged until silly levels of compression.
The admonition against using other foam is largely to prevent someone from using something too thin, as without some compression on the DAKA GRID blocks, the level of protection is lessened. As long as there is good compression, thinner foam can be used.
For larger items with protrusion, you can cut a relief in the GRID panel, as you have done, and you can even remove an entire middle panel, so long as the firearm is effectlvely blocked/supported on the remaining panels. Cutting the GRID base panel is certainly not ideal, but even with some reliefs cut for various setups, you can still configure and reconfigure around them without interference. If you want, you will also be able to get replacement panels direct.
We'll be making a usage tips video in the coming days to show how we accommodated items of various widths with the existing foam configuration during testing.
That said...as mentioned in the initial official response, we prioritized protection in test drops with accelerometer measurements, which worked best with higher levels of compression, over ease of accommodating wider items. We absolutely put quite wide systems into vault and our cases during testing using the techniques we'll show in the video, but...in reality...the level of protection provided with a little less compression is still vastly more protective than regular foam, so we are working on an even more adaptable configuration, and will do everything possible to make sure that current purchasers have an experience that works for their needs. So, buy with confidence. That said...I believe that once you see the configuration videos, 99% of users will be good with the current system as shipped. Until you get into configurations with both lights and side mounted lasers, etc., the system is accommodating-- I put my MM21E with ATACR into the system during testing.
With polypropylene cases, like 1700 series and our DAKA Hard cases, the system compresses with less lid deflection, and will naturally fit wider items with appropriate levels of compression, but we're making sure those compression levels are appropriately adjustable, as well.