If the company physically operates in the country in question, the subsidiary or branch office will have legal liabilities and contractual obligations separate of the main entity.
Since there are separate legal responsibilities, it is probably safer to serve a site that was specifically designed to match those. It also simplifies administration. If there is on issue in Switzerland it is easier if it is handled in Switzerland entirely and that means that any transactions should have happened using the site the Swiss unit controls and is responsible for. The UK site, for example, is controlled by separate unit in different jurisdiction. Staying in single jurisdiction and single unit makes everything easier.
For paypal specifically, it is IIRC in the business of money transfers, that requires registration with the relevant financial authorities and following specific local regulations. Switzerland is not a member of the EU or the EEA so local presence is probably required in some form. (The alternative would be paying some separate Swiss entity for the service.)
There might also be contractual obligations. For example, a Swiss unit of a company might have a binding contract that certain services are handled by a specific company in Switzerland. The UK unit might have a similar contract with a different company.
And sometimes there are even laws that require offering service in the local language. Which a company that has presence in the country is subject to. On business transactions (paypal is a commercial service, right?) there is also the matter of where taxes on the transaction are paid to. Many companies seem to use complex transactions to avoid almost all taxes but they still must do the bookkeeping properly. And that means knowing where the transaction happens is a good idea. An international transaction often is subject to entirely different rules.
Note that much of what I wrote above is probably incorrect. The basic idea of the issues involved should be close enough to be relevant.