Frequency response of RC circuit
In your model, the signal source is an ideal voltage source with zero internal impedance. In this case, you would indeed be able to ignore R1 and C1, and get the result you expect.

In the paper you referred to, the source is not an ideal voltage source. It's a photomultiplier tube. The photomultiplier tube will behave more like a current source than a voltage source, and it will have (like an ideal current source) a fairly high output impedance. With this kind of source, you cannot ignore R1 and C1, but must consider their effect on the transfer function. 

Aside: for this circuit, the transfer function should be better defined as 

$$H(j\omega) = \frac{V_{out}}{I_{in}}$$ 

rather than what you proposed.