For pointing loss, take a look at my answer to a link budget question, which I am amused to note contains a graph I made which is nearly identical to Figure 8.2 of Carrasco-Casado and Mata-Calvo that you linked.
Maximum gain, the highest concentration of power you can obtain, is achieved with each antenna pointed directly into the center of the other. Pointing loss is any deviation from that maximum, due to one or both of the antennas not being located at the peak of the pattern of the other antenna. That can be because
- you don't know exactly where one of the antennas is, so you're searching for it by moving the other around
- you are trying to collect more than one signal at a time, so you chose a compromise pointing that wouldn't give one a massive advantage over the others
- there is a powerful interferer in the field of view, and you decided to improve the signal-to-noise ratio (SNR) by pointing the antenna away from the real target in a way that drops a null right on top of the interferer
- the remote antenna is on a spacecraft, and you misunderstand where it is pointing, perhaps because of an error made while interpreting your telemetry, or some on-board failure
- your control over one or both of the antennas is only coarse (perhaps a subcontractor made a control interface which only accepts angles of integer degrees)
- there are other constraints that prevent you from pointing the antenna optimally, or from knowing exactly where it is pointed.
For every aperture type, there is a corresponding formula for how much loss in decibels you suffer for a given error in pointing angle. This is exactly what the $10\log_{10}(4J_1^2(x)/x^2)$ plot I mentioned above does, for a uniformly illuminated circular aperture. For a different antenna shape or weighting, you need to use a different curve, which may be purely empirical (measured, not calculated).
The exact number of radians by which your pointing is not centered, however, is not something that can be calculated, or at least not without detailed knowledge of the situation. You need to understand the model you are using, or have some statistics about how well pointing has worked in the past, or some other outside source of information about what typical means in your specific situation. The way it is generally used in practice is for antenna shape $X$, a pointing angle error $Y$ costs us $Z$ decibels of link margin, so with the current design we're okay as long as $Y<Q$.