Yes it works fine.. Alkaline OR rechargeables; black OR yellow holder. I have used the yellow holder many times when I only have alkalines handy. The only issue you might get into is if you plug a DC power source into the scanner, then the yellow holder will try to recharge whatever you have in it, the black will not. In my above example, I have to try to remember if I used the yellow holder with alkalines, and most of the time I check before plugging it in. If you never plug the scanner into DC power, you will have no issues with either holder and either type of batteries.
Bottom line is, it's not advisable to use the yellow holder with alkalines in case you forget and plug it in.