Again, if you read properly, it's referring to quotas for EU nationals being sent here on assignment
"EU/EFTA nationals working in Switzerland on assignment (with no Swiss employment contract) for more than 4 months/120 days are not covered by the Agreement on the Free Movement of Persons and are also subject to quota. For 2016, the Federal Council will issue a total of 2’250 quotas (250 for B permits and 2’000 for L permits). These quotas are released quarterly and are not distributed to the cantons."
These are people who fall outside the up to 90 days a year working in Switzerland which can be done under the pre-registration scheme, but don't qualify for a "proper" permit as they're not working for a Swiss employer. https://www.sem.admin.ch/sem/en/home...verfahren.html
This has nothing to do with any future quotas on EU nationals that might come about because of the implementation of the safeguard clause.
I guess it might depend on the canton how favourably they look on a sole trader as opposed to a GmbH or similar, but you'd have to ask the Ticino tax/migration offices. Frankly, if you're prepared to take the risk and are going to be bringing money into the economy I doubt that they'd care that much which form you choose.