Those through-holes are larger to accommodate wires for those customers who want to solder their connections directly to the board. You can see how those terminal blocks should look installed in this picture of a similar product. With a good soldering iron, you should be able to heat up both the through-holes and the terminal block leads at the same time, then feed solder in until it forms a nice fillet like those in the picture.
We do not have the mcd ratings for those LEDs. Subjectively, I find it hard to look at directly at those LEDs at full brightness. However, you might need to test them for yourself to see if they will work in any project you have them in mind for. Fortunately, they are relatively inexpensive at $4.95 for a package of ten!
The pulse widths used in the Maestro scripting language are in units of quarter microseconds and the pulse widths used in the status tab of the control center software are in units of micro seconds, so that is why there is a factor of four difference between them.