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Oops, misread the title. You can use the MyRIO without customizing the FPGA, but it's not "scan mode", but more similar to DAQmx. This article should help: http://www.ni.com/product-documentation/14603/en/
James is correct, and if you look into the express VIs and default FPGA personality you will see that it is just using an FPGA read/write node to get the current value of each input. While it shares the same basic functionality, this means that you will not be able to have a hybrid mode of sorts where you have your own FPGA application and use these express VIs without a lot of drawbacks.