I can imagine lots of customers for a PCB mill are just set in their ways and in their mind & workflow they require extremely quick prototypes. Messing with chemicals is usually surrounded by all kinds of environmental regulations so for a company it might be cheaper to buy a PCB mill compared to investing into a workspace where people can etch boards and have someone monitoring health & safety yadda yadda yadda.
That's probably true, the safety regulations can be crazy, but you don't have the same problem with a workshop equipped with stuff like a milling machine producing fine FR4 dust? At least ferric chloride isn't carcinogenic, FR4 dust is. Other materials' dusts/shavings can be fire/explosion hazards. Then you have the coolants, cutting liquids (that's mostly for machining metal, though) - those need to be properly dealt with, etc.
I would expect that an expensive dust extraction/air filtering setup would be a minimum requirement, but I have never had to comply with these regs. What are the typical rules for these things?
Then there are the usual workplace safety trainings and such, but that likely applies the same whether you are etching or milling. Getting finger burned from the etchant or cut/torn off by a CNC machine is a hazard in either case.
Nctnico's point may explain why universities like this - they don't have to deal with the regulations of chemical etching.
Note that I've found nothing that indicates that FR4 is carcinogenic but if you have a source, please post it - it would be good to know what regulatory body classifies it that way. We can compare the SDS of FR4 copper-clad with ferric chloride (links below). Both substances are, "Not classified or listed as a carcinogen by IARC, ACGIH,
CA Prop 65, or NTP" according to the SDSs by MG Chemicals. On the other hand, we see that ferric chloride causes "serious eye damage" (p. 2) while for FR4 copper-clad it says "Based on available data, the classification criteria are not met".
The exposure limits for the dust are shown on p. 5. For a vacuum/filter, you could choose a ULPA filter over HEPA if want the best in filtration but the extra fraction of a percent difference costs way more. FR4 is no picnic but on paper it looks like ferric chloride gives more to contend with, from a regulatory standpoint.
Section 11: Toxicological Information
FR4Symptoms Summary
Eyes May cause redness and mild irritation.
Skin May cause mild irritation.
Inhalation May cause nose, throat and lung irritation.
Overexposure to dust or metal fumes may lead to respiratory tract
irrititation.
Ingestion No effect known
Chronic No effect known
Ferric chlorideSymptoms Summary
Eyes Causes burns, severe irritation, redness, or pain.
Skin Causes redness, pain, or brown stain on skin.
Inhalation Inhalation of vapors or mist may cause irritation, coughing, or sore
throat.
Exposure to large doses of hydrogen chloride can cause cough,
labored breathing, and shortness of breath.
Ingestion May cause severe irritation to the mouth, throat, esophagus, and
stomach. In large doses, it may also cause abdominal pain, nausea,
vomiting, diarrhea
Chronic No known effects
Links:
SDS for FR4 copper-clad:
http://www.mgchemicals.com/downloads/msds/01%20English%20Can-USA%20SDS/sds-500-series.pdfSDS for ferric chloride:
http://www.mgchemicals.com/downloads/msds/01%20English%20Can-USA%20SDS/sds-415-l.pdf