The spreadsheet uses 2,798 RWD employee reservations, not 3,452. I'm not sure where you saw that number. I didn't make any changes to this in the last update yesterday. In search results on row 20, it says "Employee RWD res in California". If you try all 5 USA regions, you get 2,337 + 86 + 41 + 97 + 237= 2,798 for RWD. The total I use for employee reservations is 4,689 units.
However, 2,798 RWD employee reservations are still more than 2,425. Therefore the question is still valid. This is related to SR/LR availability. SR is not available yet but the spreadsheet assumes all RWD versions are available now. This problem will go away once Tesla starts making the SR version, hopefully, next month. That means some of the employees will take delivery when the SR becomes available.