The XML is the invoice — the PDF is how people read it
A structured e-invoice under EN 16931 — XRechnung, Peppol BIS, Facturae, e-arve — is pure data: seller, buyer, lines, VAT, totals. It has no layout and no field for a logo, because it is written for accounting software, not for people. Your customer's system reads the XML; their staff, your accountant and you read a rendering of it. That rendering is where your brand belongs.
Does a logo affect validation or legal validity?
No. Branding changes only the visible page. The XML aiDoks produces is identical with or without your logo, so it validates exactly the same against EN 16931, Peppol, XRechnung or Factur-X rules.
Factur-X and ZUGFeRD: the branded page is the invoice
A Factur-X or ZUGFeRD invoice is a PDF/A-3 that carries the XML inside it. The page your customer opens is your branded PDF, and their software reads the embedded XML — one file, both audiences. That is the format French and German businesses exchange most.
Invoices you receive stay as they were
The E-Invoice Viewer renders invoices from your suppliers too. There your branding is off unless you turn it on for a file — your logo on someone else's invoice would misrepresent who issued it.

