Hi , I look at this flashing at the chimney today and it is caulked using clear silicone caulking. Does this appear strange to you ? Thanks
Not correctly flashed .
Here are some pictures for you to compare the correct method .
All the best… Roy
https://www.google.ca/webhp#q=Picture+of+chimney+flashing+
Yes it is strange.
Maybe they haven’t heard of a reglet (Middle Picture):
Obvious DIY or Handyman that don’t have a clue. 
Flashings are not correct. Rigid counter flashings should be installed over the angle flashing. If surface mount counter flashings are used, then they should be caulked with a premium polyurethane sealant (never silicone).
The valley laps on the shingles are incorrect also (reversed). That saddle cricket was probably added on after the initial shingle install and I would have it monitored for leaks in the future.
That is why they left the sides of the flashing open, so the water that leaks under the cricket can come out, because the original flashing and shingles are still underneath the cricket.
I bet it did not leak. :)
Caulk and duct tape is their best friend
Side note. Check the date on your camera seems backwards
At least they tried. Unlike my inspection from last week.
Its not bad.
yes cutting into the masonry is the best but how many crickets do you see that way.
In Quebec they apply a gum edge. The flashing is not parallel, the last 1 1/2" is folded onto itself in half creating a 3/4" inch bend at a 45% angle called a gum edge. The gum edge void is filled with caulk.
look, its not a hard write up.
Calk the nail heads and observe yearly along with the roof maintenance…
JMO