Several other have correctly stated this is a dry sump motor and given good reasons why some extra oil is not of concern. ::008::
Bald Knob wrote
"Sustained high RPM cruising may force oil into the box and it will gather in this area." which is true. ::012::
I will add that the oil in the filter box due to sustained high rpms occurs
regardless of the amount of oil in the system. Too low, too high, just right, no matter. Sustained high rpms, or as Rasher said
"when the bike has been caned a bit" will cause this to occur. It's
not an indication that anything is wrong, in and of itself.
Repeated suggestions have been offered to check the oil in the manner described in the manual. They are referring to the
owners manual that every bike came with, not the Factory Service Manual that costs around $90, so please dig out that manual, or go to the dealer and get one if you don't have one. It's a very useful reference tool.
The reason people are suggesting this is that the dry sump design makes it very unique to identify when the sight glass is providing a useful "measurement". The procedure is outlined in such a manner as to provide a uniform method that matches what Yamaha came up with to check their design. It's still not gospel or any real "measurement", but does provide a more useful bench mark by which you can guesstimate if you need oil or not. Think of it as checking to see if the goldfish are still alive. See oil, they're good. No oil, likely you should add a little.
Note that the Super Tenere, along with most Yamaha motorcycles, has a low oil
LEVEL light, not a low pressure light.
In your case, because you don't know how much oil you put in to begin with, it's probably worth the trouble to check the oil exactly as described in the owner's manual so you can have some idea if it's hugely overfilled or not. If there is any air showing in the sight glass after following the procedure, stop worrying about it and just ride. Next oil change, consider actually measuring the amount you put in and putting in the correct 3.6 quarts, (ok, actually specified on page 7-14 for oil change with filter change as 3.59 US quarts or 3.4 Liters or 2.99 Imperial qt), for when doing a normal oil and new filter change.
You can buy plastic oil measurement cups at most motorcycle dealers that sell dirt bikes. Pretty cheap if you want something larger than a cooking cup measurement and handy for many moto related things. Don't use the wife's Pyrex measurement cups!
The owner's manual outlines the procedure on page 7-12 as follows:
1. Place the vehicle on the center stand. A slight tilt to the side can result in a false reading.
2. Start the engine and warm it up for ten minutes until the engine has reached a normal temperature of 60º C (140º F), and then turn the engine off.
3. Wait a few minutes until the oil settles, and then check the oil level through the engine oil level check window located at the bottom-right side of the crankcase.
TIP
The engine oil should be between the minimum and maximum level marks.
4. If the engine oil is below the minimum level mark, add sufficient oil of the recommended type to raise it to the correct level.
One might note that they make no mention of if it's too high. 
Probably because that is not of much concern on a dry sump design, since the engine can only take what it needs and that amount is static, pumped thru and back to the reservoir.
