On my Adventure I have Hobie extension tubes for the rod holders and I always have rods in them when I sail. i have been sailing MD kayaks for around 9 or 10 years now the following are my thoughts and experience:
The extensions give a greater 'spread' so there's a bigger gap between the rods and i do not find that they get in the way at all really when I'm sailing. Occasionally the sheet hangs up on a lure but that is very occasionally and usually not too hard to cope with.
And one time the sheet got caught under a reel handle and flicked the rod out of the holder and into the water (fortunately my rods are ALWAYS secured to the boat so it got wet but I didn't lose it) - I think that was before I got the extensions though.
The time to watch out is when you put the sail up (assuming you have it stowed and only raise the mast when out on the water); that's when the sheet lifts up from the deck and can catch under a reel or a line guide and lift the rod; it is also the time that you realise that the lead of the sheet is going through, under or round things on the stern deck - which obviously you need to sort out before getting under sail.
So my rule of thumb is - there is some 'overlap' between sheet and rods but as long as you use your noggin (w.r.t. sheet leads and thinking ahead), and as long as you have all rods tied to the boat, it shouldn't interfere to any extent that would detract from your enjoyment of or ability to sail.
...now vertical rod holders on the aft deck as I have seen on some kayaks would be a different matter.
Hope this helps.
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