We are talking about a war situation here, not peacetime, and it appears to be accompanied by an absence of regular mint controls such as a pyx trial, for which there is no evidence. The engraver will accompany the troops, who were only paid when a supply of coin or plate silver was available to coin. Levies were made on the local populations to pay the troops defending them, or wealthy individuals were encouraged to donate plate (which was how most wealth was held) for the King's cause. This was then either distributed or melted to produce coin. Royalist mint coin production appears to be a real roller coaster with periods of inactivity followed by frenetic activity when demand rose. Somehow, they had to find coin for the troops, who were always owed money, and this was satisfied on an occasional basis. Clearly, if coin was available there would be no reason to produce coins, but with the war effort effectively funded by the wealthy aristocracy, they held plate which was donated and melted down. e.g in Besly's 1992 article, Vyvyan's mint record books at Exeter list the quantity of donated plate and from whom in detail.
The evidence of incompletely erased underlying detail tells us that dies were reworked. The main Royalist denomination was the halfcrown, because they always had a higher ratio of cavalry to foot soldiers than did Parliament. Half a crown was a day's pay (assuming they did actually get paid). However, the larger dies used on the pound, half pound and triple unite were redundant by 1644, probably following the closure of the Oxford Parliament in April 1644 and the dispersal of those Royalist forces to York and the south-west, though crowns continued to be struck at Exeter until the following year. This left dies with a diameter of approx. 2" with no application requiring the full surface area.
I'm sure they did mark out a circle for the legend, just that I don't think they were concerned about complete accuracy of dimensions. Hammered coins are regularly struck off centre, so there isn't the compelling demand for the neat obverse and reverse you see on milled coins and a discrepancy of a few mms in diameters would not be as important as paying the men. Holding stock is a reasonable premise in the case of a fixed mint, but in the Civil War you have a mobile facility. There is plenty of evidence for die movement between locations over what can only be a period of months. Punches appear to move in groups, which is what you expect as they would be the property of the engraver, just as engineers today would have their own set of tools. Their punches didn't contain a complete set of letters and numbers as would be desirable in a fixed location, rather, many characters are composite made from smaller shaped punches. The number of engravers involved is small, probably only 6 or 8 based on the punch sets and marks employed, and they would all follow the troops. Only Shrewsbury then Oxford, York, Bristol and Truro then Exeter can lay a claim to be 'permanently open', and even that was only a little over a year in the case of York. Oxford as the capital had a significant full time garrison from December 1642 through to surrender in 1646. Vyvyan's mint at Truro in 1642-3 and then Exeter from Sept 1643 on can reasonably be said to be open throughout, but the surprise defeat of Essex at Lostwithiel and the elimination of Parliamentary forces from the south-west in August 1644 resulted in the demand for coined specie collapsing. That is why there are 1645/4 crown dies. The sudden reduction in demand meant the dies stayed on the shelf for a year until the war revisited the area.
With the continual movement of troops around the country, there would inevitably be areas where it was impossible to source the metal bar required to produce dies, so reusing them was a necessity. Where they went was dictated by military activity and wasn't ordained in advance, so prior notice of an intent to purchase bar stock couldn't be given. Again, it works ok in a fixed location such as the Royal Mint, but not in deepest Shropshire when you happen to have overrun a Parliamentary supporter's mansion, and purloined his plate. Coin production in this instance is reactive and not proactive.