"VISA and MASTER cards fall into "Magnetic cards" category, while telephone cards are chip based,"

In the UK, Visa & Mastercard are increasingly including both chip & magnetic stripe on their cards.
I think the "chipped" Credit Cards are particularly popular in France?

What exactly do you mean by "telephone cards?" - are you talking about GSM SIM cards, or some sort of payphone payment card?
The GSM SIM interface is defined in the ETSI specs - which are downloadable for free!

"The in-depth information you are looking for is generally confidential."
Data communications formats between card & reader are specified by organisations such as the ISO - so, while they're not actually "confidential," you do have to pay to obtain copies.
I posted a link to a source of mag stripe info recently - try a Search for "Credit Card"

As for the protocols for obtaining Credit Card Authorisation, these are proprietary and you'd probably need to obtain a licence (they obviously don't want to give it out to any old Tom, Dick, or Harry!)