Ask the installer to give you some references.

It is not uncommon but your concerns are certainly valid. The capping can make the current siding look a bit inorganic after application.

It is quite common to do an L caping opposed to full capping when you have wood siding. This way the wood window trim matches up with the wood siding.
An L-cap just means the area where the storm window was removed would be capped with aluminum in order to cover up any of the imperfections from ripping out the storm window. This is a very small area and looks as if its part of the window while keeping the exterior wood trim untouched.
Keep in mind, you need to still paint/ maintain the window trim so no moisture is absorbed and also to keep the wood from drying out and splintering.

This post was edited by mmarse1 on Mon, Feb 24, 14 at 11:33

+1 . The method that Marasel describes is also called a "blind stop" trim. You could also paint that area if you'd like...
How old is your home? The reason that I ask, is many installers will mandate an exterior installation with trim sinply because lead safe procedures are much more costly and invasive when doing an interior installation (interior woodwork is removed as opposed to doing demo from outside). If your home is older than 1978, make sure that it is either tested for lead or your installer is a certified lead-safe renovation firm.

I know when they rip out the storms they will caulk any of the old screw/nail holes and I'd be responsible for touching up those areas with paint. Sounds like I can do that or the blind stop as mentioned above. I'd love to get the exterior of my house as maintenance free as possible while also keeping it's looks up to par, so I'll ask the sales guy about that possibility and see what he says about how it would look on my particular home.

As far as the lead, my house was built in 1970 and they are lead-safe certified and would charge $75 per window if lead is found. I'm really hoping it doesn't come to that, but with two little girls it is what it is.

In 1970 it wouldn't be a bad idea to test. Good chance that you don't have it.

+1

I haven't seen a home in the 1970s that had lead yet.

Doesn't rule it out but becomes less likely for certain.

Absolutely, lead in a home built in 1970 would be very rare.
Also, there isnt a whole lot of dust from a replacement window application to begin with even with lead but most guys are certified now.