The vertical wall seams crack more readily because the house shifts and moves. Ive tried grouting only and going back to caulk with sanded grout caulk or silicon only after a crack develops, hoping in some cases it will not. Sometimes it does not crack. Some contractors caulk all seams as a matter of course, no callbacks, safer. I liked the idea of sanded grout caulk to match your grout color It has not held up for me in wet conditions, such as the top of the bathtub where the wall tile starts, etc. , definitely not along the shower floor where the wall tile starts. It has held up in other areas though, and looks nicer when it all ties in. I agree, mildew on silicon is unsightly. Every bathroom has different conditions, including ventilation, moisture, etc. Some people have to clean out and recaulk the silicon every year or two. Whether its allegedly mildewproof silicon or not.

It's not to stop the water-- it's to keep movement between the tub and the walls from cracking what would otherwise be a grout joint.

Update on my dilemma, I filled the gap with clear silicon and covered with a strip. I didn't notice until I opened the strip that it was almond color, not white. For the corners I cut the strip in the middle fold and it adhered pretty good in the corners. It will do for now. We plan on converting to a shower with no tub sometime before the end of the year so that's okay.

I did confront them and they came back to fix it.  This was the fix.  They hacked up my tile so bad, I didn't want them doing any more. The caulk I used 2 years ago was Dap Kwik Seal Ultra caulk, I believe.  There was no sanded caulk underneath.  We got it completely out before laying down new caulk. I ended up getting as much out as I could, drying it out completely and putting new caulk over the top around the tub and just cleaned up the caulk lines in the corners.  I would have waited but the kitchen demo started today and I couldn't go without a kitchen sink and a tub.  I figured the worse case scenario was it wouldn't stick.   It didn't turn out too bad for a DIY.  Definitely better than the contractor.   It may need to be redone after the kitchen remodel is complete but I'll be no worse off then I was when I started. P.s. Great tip about taping before scraping.  If it ends up that I have to redo it myself, I'll be sure to do that