Hmm. If your fill plug really is lacking the dipstick: looking at the photo above, it seems that the transmission dipstick could be used as a temporary substitute, with that shoulder at 6.25 inches indicating four quarts.
I don't think anyone has ever defined if the plug should be screwed in when measuring the oil level but I've decided on the following for my use: Threaded plug, just rest it on the last thread without screwing it in. Push-in plug, push it in to get the oil level. If anyone has a link to Yanmar's recommendation on this subject, I'd like to see it.