Although the word IT is mentioned, I highly doubt that here, in a text talking about ERP as a whole, the wording "transparent process" refers to some user-invisible part of the implementation of that software.
On the contrary, reading up on Enterprise Resource Planning, wikipedia mentions:
ERP now covers more functions and roles—including decision making, stakeholders' relationships, standardization, transparency, globalization, etc.
ERP systems centralize business data, which [..] [b]rings legitimacy and transparency to each bit of statistical data
I don't think invisibility is meant in either of these sentences...
So the process in the mentioned paragraph seems to be the business process, not the in-memory-running-abstract-special-kind-of-computer-program process. I would thus go for the "normal" meaning of the word, unless someone (maybe one of the anonymous downvoters) can convince me that a process in the context of enterprise resource planning is supposed to be invisible :)
A process is transparent if it is clear to an observer what it involves.
It is the opposite of an obscure process, which can be described as a black box: we know what goes in, we know what comes out, but we don't know how the input get transformed into the output.
Transparent processes are usually seen as very important within companies when it comes to communication, escalation, etcetera. What people envisage when they strive for a transparent process is that they know all the steps involved in a process, and that they can see at which stage of a process a specific case is.
What it means in your sentence though, is a bit hazy. It seems to imply that there might be extra costs if the process is transparent enough, which in turn implies that hiding what you are doing could save money. That does not sound good :)