Boyle's law as you stated it, applies 1) where temperature is constant, and 2) at a particular moment in time; it is not dynamic.

With most smokeless propellants, the rate of conversion from powder to gas increases with both temperature and pressure. So, in a smaller space, temperature and pressure build more quickly which accelerates conversion at the time when there is more unconverted powder still in the case.

In the example using 38 Special, the pressures you derived seem very close to published figures, but note that in the Speer Manual #11 (and many subseqent editions) there is a report in the section on 9mm about making sure there is sufficient neck tension to prevent bullet set-back because it can create dangerous pressure noting that bullets intentionally seated just 0.030 inch deeper nearly doubled in pressure and I don't think that follows a static Boyle's law analysis.