I also have this kit, but have not started it. However, I am 1/2 way through building their Bismark kit. And guess what? It has the same flaws. The deck has huge gaps in it as well as many of the seams on the deckhouses. The V-Strut and shaft housings on the lower hull are really poor fits.
For small gap filling, instead of white glue which I found leaves depressions and airholes, I use both a medium CA or 3M Porcelin Cement. Both these products allow you to fill a crack, both horizontal or vertically, without much sanding.
My feeling toward raised deck lines are like those the wingy thingy modelers have towards raised panel lines. They don't exist. So, since 1/3 of the deck lines are sanded to oblivion due to the seams, I am just sanding the entire deck and rescribing.
I have salvaged raised panel and deck lines with streched sprue cut to length, positioned, and glued in place.
Scott