Yes, the very meaning of PE is that only locally sourced profits might be taxed.
Having a registered PE of a foreign company could lead to following scenarios:
1) PE is registered but not treated as a PE for tax purposes. This can be the case when PE registration is done only because for example when you a hire an assistant, who doesn't do sales. No Corporate taxes apply, only payroll taxes are withheld because hiring the person in Estonia.
2) PE is registered and treated as a PE. CIT applies, but its only paid when the profits are withdrawn from the PE. Not for example when profits are reinvested to Gold plates and kept safely in the Estonian office.
3) a foreign entities PE can also be registered if the foreign entity is purely passive in Estonia, for example as a passive partner/investor of an unincorporated partnership, managed by a 3rd party. In such case the unincorporated partnership obtains a tax number in Estonia, which technically is a PE. Estonia only taxes the local profits of the partnership, while this partnership might operate in other jurisdictions too.