It would be nicer to cover it if you want a clean look. Problem here is the spot where the holes are might be shift up which makes your tile unlevel. It might be a sore eye for you looking at it.
I try to would cut holes in the tile to match the raised pieces so it sits flat, if you want to get really fancy you could sand the piece you cut out to be thinner and use them to cap the holes afterward ...
Oaky so after putting tiles in my tank is been 3 weeks now tat i have tiles in my tank, 4 days ago i did a 60% water change and now my water is really cludy and not clear at all.. The tiles are my in my 180 gallon 6x2x2 acrylic and i am running two FX5 for filteraton...
Before the water change the water seem clear...
TILES HAVE BEEN WASH AND WASH BEFORE PUTITNG IN THE TANK..
i don't have any problems with food getting stuck under the tiles. There are some wastes stuck under the tiles and between the cracks. I am able to siphon out the wastes between the cracks during waterchanges. I figure I might need to lift the tile up once or twice a year to do a thorough cleaning but it's still easier than siphoning poops on the sand surface weekly. My theory is that these tiles are poreous so ill have extra beneficial bacteria will grow in it.
The tank has been running since the day I made the post and no issues. I don't feed sinking pellets and my pleco also does a great job cleaning.