The definition of echo time (TE) in MRI is the time difference between a 90-degree RF signal and the echo peak, which feels like an intrinsic property of the proton.
How can we even control how long does it take for the echo peak to happen?
The echo peak is not an intrinsic property of the proton. The echo time describes the magnetic environment, which can be manipulated. Specifically, there are two types of echoes in MR.
Gradient echoes form whenever $\int G(t) \ dt =0$ where $G$ is the gradient waveform.
Spin echoes form whenever $t=2\tau$ where $\tau$ is the time between excitation and refocusing.
So we can control both when a gradient echo occurs or when a spin echo occurs.