Using Matlab/Simulink to build Reader based on Software Define Radio
You probably can. But: the AD9361 is definitely a complex beast, and I honestly think you're setting yourself up for more trouble than your solving when using a model of a device with a couple thousand different settings.

Unless you're planning to build an SDR out of an actual AD9361, I'd recommend not using them in a simulation. It's probably among the most complex models available in Simulink!

You shouldn't be building your own SDR, but rather buy one; as far as I remember, these typically need relatively high bandwidth, and designing the digital side of a PCB that carries multiple Megasamples of complex data per second into your computing unit will not be a beginner's project (aside from being far more expensive to buy and manufacture in single digit quantities than just buying a commercially available SDR).

The question really is whether you need to have a simulation that incorporates the actual SDR hardware – wouldn't for a very long time a simple idealized (IQ) mixer be representative enough? Aren't you starting off at the wrong end by trying to model something that works quite close to ideal very intimately instead of trying to get a system understanding based on idealized models?

For example, your flow graph top row isn't correct, to be honest. You used "QAM modulation" for what should be a quadrature modulator (QAM modulation is a baseband symbol mapping method, not a "modulation" as in "shift of frequency").