Yes, physics majors have a high rate of PhDs. However, physics majors are often such a small portion of students that the comparison has little meaning for the purposes of thread questions.
While stats are rarely ideal, clinging to assumptions that are not based on any supporting reference or evidence and conflict with stats is generally less reliable. The original claim was, "The reason top LACs produce a lot of PhD students is also because they generally lack engineering programs. " Many top research colleges have few students pursuing engineering (5-6% at Harvard/Yale), and the reported PhD rates from those engineering colleges are often higher than the overall rate for the school, such as the PhD rates listed for Cornell’s engineering school below. Note that soon after graduation, Cornell Engineering students have a higher PhD rate than any other reported Cornell college. The rate of Cornell Engineering PhDs soon after graduation is higher than Cornell overall long after graduation.
Most of the reports I’ve seen separate the different colleges at Cornell. Some specific numbers are below, comparing Cornell to some of the discussed LACs. Cornell does indeed appear to have almost as many advanced degrees as LACs similarly selective LACs. Cornell had generally similar rates of professional degrees (Law, MD, MBA) and a higher rate of master’s. The only area were Cornell was notably lacking compared to selective LACs was rate of PhDs. Of the 8% reporting PhDs at Cornell, 33% were in biology, 25% in engineering, 16% in social sciences, and few in other fields. Even if all the biology PhDs were from A&S and not Life Sciences, the A&S PhD rate at Cornell would still be well below many selective LACs.
Swarthmore: Shortly After Graduation – 21% advanced degrees, 9% PhDs
Amherst: Shortly After Graduation – 19% advanced degrees
Cornell: Shortly After Graduation
Ecology – 33% advanced degrees, ? PhDs
Engineering – 32% advanced degrees, 9% PhDs
Arts & Sciences – 27% advanced degrees, 7% PhDs
Life Sciences – 22% advanced degrees, 3% PhDs
Industrial & Labor Relations – 14% advanced degrees, ? PhDs
Swarthmore: Long After Graduation – 80-90% advanced degrees, 32% PhDs
Amherst: Long After Graduation – 80-90% advanced degrees, ~20% PhDs
Cornell: Long After Graduation – 78% advanced degrees, 8% PhDs
Arts & Sciences – 82% advanced degrees
Ecology – 81% advanced degrees
Industrial & Labor Relations – 78% advanced degrees
Engineering – 77% advanced degrees
Life Sciences – 71% advanced degrees