I can't, think of any reason why not, so long as you apply for the Licence to the same National Authority that issued your Medical, and use the application form issued by that Authority.
So, for instance, Swiss Medical, Swiss TK/Written Exams, Portuguese Flight Training and Skill Test, all recorded on Swiss application form, then apply to Swiss National Authority for the licence.
Just be sure that everyone involved understands that you will be applying for a Swiss issued Licence, as the paperwork may be slightly different. For instance, a Portuguese Flight Examiner will have to have a National Briefing from the Swiss authority.
Frankly, I fail to see why EASA Licences are at all associated with individual National Authorities. It seems to defeat the whole point of having a common Licence.
MJ
