One way the OP could answer their own question would be to perform the comparison, of their setups 1 and 2, in their own lab. For various reasons, this may be infeasible. But other options exist, e.g., optical calculus-based computer simulations and simple manual calculations, as shown here.
Alternatively, it is not difficult to perform an actual experimental comparison of setup 1 and 2. It should be noted that attenuating a high power laser beam is not the same as attenuating a low power laser beam. Aside from safety considerations, factors such as optical component damage thresholds must be considered.
With that important caveat, consider the breadboarded system below:

The laser, not yet powered up in the photo, is a USB-powered 10 mW diode laser with measured wavelength of 485 nm. It is already somewhat polarized, but not very well. The laser beam passes from left to right through a calcite polarizer, an adjustable iris aperture, the rotating optical component (either a half wave plate or a calcite polarizer), the calcite analyzer polarizer and finally is incident upon the photodiode. The two fixed orientation polarizers, on either side of the rotation mount, have their polarization axes aligned. As well, the diode laser was initially rotated so that its polarization axis aligned with those of the fixed pair. Consequently, transmission is maximum and attenuation is minimum if there is no optical component in the rotation mount.
In the photo, the calcite polarizer is mounted in the rotation mount, as per setup 2. The photocurrent from the photodiode is manually measured using a digital multimeter in ammeter mode.
The next photo shows the system when the diode laser is powered on and the calcite polarizer is in the rotation mount.

All that remains is to measure the photocurrent as a function of rotation angle of whichever optical component was in the rotation mount. This was done for both setup 1, with the 488 nm half wave plate (HWP) in the rotation mount, and for setup 2, with another calcite polarizer in the rotation mount.
Data were collected manually for every 10 degrees of rotation of the respective optical component. To facilitate comparison with the expected intensities versus rotation angle, the photocurrents were normalized by 1.57 mA, for setup 1, and by 1.52 mA, for setup 2. The raw (unnormalized) results are shown in the table:

Plotting the normalized photocurrents versus the rotation angle yields the following figure:

This confirms the OP’s intuition: setup 2 provides better control of the laser attenuation. Furthermore, polarizer transmittance is not a factor with the calcite polarizers used here. This may be an issue with lower quality polarizers, but those would not be used to attenuate a laser beam of, say, 1 W power.
Experiment notes:
Since I made the photocurrent measurements every 10 degrees of rotation, I did not make measurements at 45 or 135 degrees. It would not matter for setup 2, but it would be useful information for setup 1 because attenuation is maximum there. So I did the two measurements, with these results: 0.0353 mA photocurrent at 45 deg and 0.0348 mA photocurrent at 135 deg.
In setup 2, it was easy to attenuate the laser to the point where I could not see any transmitted light. With setup 1, this was not the case: even with maximum attenuation, a little light was transmitted. The data show this as well. My hypothesis is that this was due to the facts that the 485 nm laser center wavelength is not exactly the same as the 488 nm HWP wavelength and the diode laser’s bandwidth is significantly broader than that of the 488 nm argon ion laser line, which is what the HWP was intended for use with.