That's a very interesting question. I have a few comments:
Consider resale value. Four Winns owners put a high premium on horsepower. When I bought my boat at 12 years old, the books values were about $3k higher for a higher horsepower option. It stands to reason that a 5 year old used boat would have an even greater premium value for the higher horsepower.
I'm with you...it would sure be nice to buy the 300HP and "convert" it to 350HP by having the software changed / tuned. I'm not sure what that would cost. If you cannot find anyone who has done it online, then it may not be as easy as you would think.
Consider warranty. Changing the software/tuning would most likely void the warranty, so would you wait until the warranty is over? or just screw the warranty?
Fuel usage is not really a factor. Both engines will use the same amount of fuel at the same speed. So cruising at 30mph will use the same fuel with either engine. However, if the extra HP leads you to cruise at higher speeds, then you will use more fuel accordingly. At wide open throttle (WOT), the 350 will use about 17% more fuel per hour, but nobody cruises at WOT.
Is 300HP adequate? Yes, for most purposes. You'll wish you had more horsepower when pulling up a tube or skier when you have 7+ passengers on board. You'll wish you had more horsepower if you are racing your buddy and he beats you by 2 mph. You will never wish you had less horsepower.
I would work out your best deal with the options you want and the 300HP. Then use what you know to try to get the best deal on the 350HP. If you get the difference down to $3000 or less, I would go for it. If it's still $5000... I don't know.
By the way, my H240 has the 250HP carbureted engine, and performs quite well. However, my H240 (1996-1999 style) is 4000 lbs, where your 2017 H260 is 4900 lbs. Both are rated for 13 passengers (but I don't know where I would fit that many people).
Ray
_________________

"Knot Easy" 2000 Horizon 240 Volvo 5.7GS /SX
tow: 2017 Honda PILOT EXL-AWD
prev. boats:
'87 Chaparral 198CXL 4.3 OMC Cobra
'69 Jetstar 16ft Ski Boat, 115hp Yamaha
'68 Aluminum Jon Boat, 3hp Sears
'64 Water Wings