Because it is meant to avoid 2+ European patents on the same subject-matter, otherwise a third party will have to get 2+ licenses for the very same subject-matter, which is unfair given that they are for the same invention. With Art. 54(3) EPC limited to European patents you could have the same monopoly in the Contracting States of the EPC and somewhere else, and that somewhere else is not a problem because the third party needs the license per jurisdiction.
You can find a lengthy discussion about this topic in the Travaux Préparatoires of EPC 1973 here. In the Travaux Préparatoires of Art. 54 of EPC 2000 you will find the following:
- Pursuant to Article 54(3) EPC, in order to preclude double patenting, European
patent applications having an earlier filing or priority date than the filing or priority date of a second European patent application, and which are published on or after the filing date of that second application, are considered to form part of the state of the art for the purpose of examining the novelty of this second patent application.
You will also find that, with EPC 2000, former Art. 54(4) EPC (1973) was deleted, which limited the scope of novelty-destroying European patent applications to applications commonly designating the same Contracting States. Before EPC 2000, you had to designate each Designation State individually and pay for it, and as long as your application did not collide in Designation States with the Designation States of an Art. 54(3) EPC application, you were good to go. With EPC 2000 the designation system changed, now all the States are designated and you have to withdraw designation if you want to do so, but you pay a flat Designation Fee for all the States. It is irrelevant if the two applications do not designate the same States anymore, a previous European patent application is Art. 54(3) EPC for the later European patent application.
The requirement of paying the fees in a PCT application and filing the translation if the application is not in English, French or German to become Art. 54(3) EPC prior art is, again, to avoid double patenting. While these requirements are not met, the PCT does not pose a threat for double patenting.
It is not part of the question, but seems worth mentioning. Most if not all Contracting States of the EPC have a provision analogous to Art. 54(3) EPC but for national patents and patent applications. The reason for its existence is the same, a country does not want to give 2+ monopolies for the same invention. This could be a problem for a European patent when validated in a State because there might be a national patent application that is relevant for the novelty of the claimed subject-matter in that particular State. Rule 138 EPC comes to the rescue here:
If the European Patent Office is informed of the existence of a prior right under Article 139, paragraph 2, the European patent application or European patent may, for such State or States, contain claims and, where appropriate, a description and drawings which are different from those for the other designated States.
You are to make the claims of your European patent more limited only in those particular States so that the validation does not have a conflict with earlier national patent rights.