The world of flight ticketing is pretty complicated, and a lot of the folks here understand it pretty well.
Unfortunately that means if you use words like ticket, coupon, PNR etc they will take it at face value by what those terms technically means regardless of how a lay person might see it.
To you, it seems that there are two different ways of making the booking, but as you have been told here, the actual ticket you get as an end result is effectively the same if we can rely on what you have told us. A single PNR (the six letter code) matched to a single e-Ticket number starting 125-xxxxxxxx (even if there are some different numbers in the last two digits sometimes, often referred to as coupons) is one journey and will be fine for through checking baggage and IRROPS (problems).