Hi Tom, I think with a little extra care you guarantee a good long term waterproof seal. The window itself is probably impervious to rain inside or out. They're made to channel water to the outer weepholes, even if it accepts water from the inside. The real concern of course is getting water to that sill plate underneath if your caulk fails.
I start by leaving the CBU 1/8" to 3/16" away from the window to create a cavity you can fill up with high quality silicone (that's seal #1). I like to use Hardi for the sill because it doesn't allow water to pass thru the core. Next the whole window gets CBU tape, thinset, & then 2 generous coats of Redgard. The Redgard is ramped right up onto the window frame a little bit, both coats (seals #2 & #3). Make sure you put a positive slope on the whole sill
before the Redgard to keep the water rolling away from the window. Next I put a generous bead of silicone above the Redgard at the window (seal #4). Then tile & leave it 1/16" away and fill that gap up with silicone (seal #5). Make sure to preserve that positive slope away from the window in your finished tile. You need to keep that water moving in the right direction.
The protected seals underneath will last longer than the shower if you exercise even minimal care to maintain that top caulk every 15 or 20 years.
If you have an opening window it does become a cleaning nightmare like Paul said. If so, I would consider changing it to a fixed window if it was my house.