Η σύντηξη του τελικού -ν μαζί του πρώτου σύμφωνου της επόμενης λέξεως.
I have heard the final -ν of some words completly merging with the next consonnant, like for instance τον καφέ isn't pronounced /ton.ka.'fe/ but /to.ga.'fe/, I know that it gets silented before μ or another ν, and that it's pronounced /m/ before β, μ, π, φ, ψ and the digraph μπ, but I want to be sure whether its merging with κ, π, and τ to form γκ, μπ, and ντ is not too informal or associated with a certain accent.
I want to be sure whether its merging with κ, π, and τ to form γκ, μπ, and ντ is not too informal or associated with a certain accent.
It's not. It really is a naturally occurring phenomenon for native speakers in everyday speech. It's a bit of an inside joke as well, the fact that usually no one takes care to enunciate enough to produce distinct sounds that correspond to the actual letters. So, if you want to call your friend Peter, θα καλέσεις τον Πέτρο > το Μπέτρο, and then someone may ask you "Τι κάνει ο Μπέτρος;" :P
In my experience (I'm an Athenian), the people who enunciate these final -ν + consonant nouns in casual speech - not careful/forced enunciation- are usually people with an accent. What I mean by that: when I think of my Cypriot friends' accent, I think of the specific way they pronounce the phrase 'την πόρτα'. I'd say 'τη μπόρτα' but I'd expect to hear 'την πόρταν' from them.
In short, don't worry too much about it. All accents are beautiful and however you say it, it will be correct. :)
From the top of my head I can think of two examples, one for each. - For μψ, μεμψίμοιρος: both consonants are pronounced as you see them, the μ maybe not very clearly, listen here https://forvo.com/search/%CE%BC%CE%B5%CE%BC%CF%88%CE%AF%CE%BC%CE%BF%CE%B9%CF%81%CE%BF%CF%82/ For γξ, έλεγξα (simple past of ελέγχω = to control): it sounds like νξ/nx, listen here https://forvo.com/search/%CE%AD%CE%BB%CE%B5%CE%B3%CE%BE%CE%B1/. Also ν instead of γ for ελέγχω.
Edit: Do you have any specific words in mind for these combinations?