The Philippines don't seem to participate in the PEPPOL network, no. A list of all supported countries can be found here: https://www.odoo.com/documentation/18.0/de/applications/finance/accounting/customer_invoices/electronic_invoicing.html

I'd say you've got two options (or maybe just one):

1. Inter-Company transactions are defined on a per-company basis. This means you can have your Philippines company use that feature while others don't. Based on your post these seems not entirely applicable since you seem to send and receive invoices in all directions or from/to all companies
   
2. You can define - per contact - what the default mode of sending invoices should be (Tab: Accounting -> Invoice sending). When an options (other than 'by PEPPOL') is selected here, Odoo wont sent invoices to the PEPPOL network for this customer (which would be the desired configuration for your 3 companies in Belgium)
   
   Odoo may just tell you that the recipient could receive PEPPOL invoices:
   
   This by PEPPOL checkbox, when sending an invoice, could also just be manually unticked, if the frequencey of inter-company invoicing isn't too high anyways