Regardless of all the factors affecting boat speed, the single biggest factor is waterline length. The longer the waterline, the faster the boat will be all other things being equal.
In theory the PHRF ratings are given in seconds per mile. Thus Boat A with a rating of 200 should be faster than Boat B with a rating of 203 and at the end of a mile long race course, Boat A should be 3 seconds ahead of Boat B. The operative words are "in theory." Nonetheless less the ratings are reasonable estimates of relative potential boat speeds. Small differences in ratings, say under 15 are not all that accurate.
A factor you have no control over is the weather and diurnal wind variations. Most beer can races are held in the evening and as the evening progresses towards sunset the wind speed typically declines, thus the slower boats spend more time in less wind going more slowly than the faster boats. One way to reduce this effect is to use Time-on-Time corrections rather than Time-on-Distance, it helps but doesn't solve the dying wind problem. The bigger boats will always have an advantage.