I encounter the same issue on my 1996 1500 SE where the cam gear would rotate when tension was applied and not the crank. Logic (my own) said to start the cam gear an amount equal to this movement below the mark before tension so the final setting has all marks aligned. Performed this on both sides and after tensioning I rotated the engine several times from the crank (plugs removed) and verified all marks lined up exactly, which they did. My take is that it would be important to have all marks lined up. The engine started with out any trouble or unusual noise of valves slamming piston tops. - BUT I DO NOT RECOMMEND THIS AS A SOLUTION YOU MUST MAKE YOUR OWN DECISION. I have driven the bike +1000 miles without issue.
I will probably open up and re-inspect to verify alignment has been maintained. Not something I am looking forward to but it will make long trips less stressful.