Who first developed this concept of a covenant of grace?
Much like the doctrine of the trinity, to proponents of the doctrine, the answer is, "It comes from the Bible." But obviously the actual historical development and refinement of definitions is less straight-forward than that. But do keep in mind that to those explicating covenant theology, all they're doing is teaching what's in Scripture.
It's hard to pin down exactly who was first. Heinrich Bullinger, Huldrych Zwingli, and Johannes Oecolampadius all wrote letters and delivered sermons in the 1520s about the covenant of grace. They are difficult to date with precision. In the case of Oecolampadius, he was teaching the covenant of grace as an "outworking" of the covenant of redemption (though he does not explicitly name it) in 1521.
Reformed theologians contend that Martin Luther's law/gospel distinction, first developed around 1525, is just another way of speaking of the covenant of works and covenant of grace.
From what I can tell, the two most commonly cited as the originator of the covenant of grace are Bullinger and Oecolampadius. In my non-scholarly opinion, I'd give the edge to Oecolampadius.
Were the other two metacovenants developed at the same time?
Roughly. The ideas are implicitly there (even as early as 1521, as I mentioned above). The covenant of grace assumes a covenant of works (or else, what is there to be gracious about) and also a covenant of redemption (or else God was blindsided by humanity's fallenness and made the decision to intervene temporally rather than eternally). But it took some decades before all three ideas were talked about simultaneously, as part of a "package deal." The order seems to be that first the reformers were eager to talk about grace (often "using the covenant of grace as a summary of biblical theology"), then started discussing the covenant of works as a "creation covenant," then developed the doctrine of the covenant of redemption to round it out.
Zacharius Ursinus, one of the authors of the Heidelberg Catechism, is credited as one of the originators of the idea of the covenant of works in the 1560s. Johannes Cocceius is credited as an originator of the covenant of redemption around the same time. Coeccius, Ursinus, and Herman Witsius wrote systematic theologies in the latter half of the 17th century organized around the three covenants.
Are there differences from how the Covenant of Grace was first conceptualised and how it is understood now?
No substantial differences I'm aware of. Though I haven't read the primary sources pre-1700, I've never read any indications that it underwent significant changes through the years.
I consulted these works to write this post: