Doing the physical with two computers should be fine. However just like most things, it will work fine until there is a problem. One of the things that we use for physical inventory is a batch device, this allows users to scan particular areas of their store and then import these files. Typically when someone does this we recommend that they do their inventory in small chunks. This allows you to import these small files and then make sure that everything looks Ok. If there is a problem (someone scanned the wrong barcode, something is not being found in inventory etc.) it makes it easier to find where the problem item(s) are.
When you are scanning directly into our Physical Inventory Control System (PICs) from two stations, you will get data that is intermingled. So if there is a problem it could be harder to find. So if you are going to do this, take it slow and check the file periodically. We have made some improvements to PICs that will allow you to more quickly see when there is a bad item in the PICs file. When you scan something and it is not found in inventory, the description field that shows up will be blank. If you see this you should probably stop the scanning and go see what the problem is.