Rules source? I have yet to see one stating that you can't. It merely takes a free action per shot called. If you're taking the time for four take aim actions (one to negate range and three for the +1 bonus), that's two full action phases, plenty of time to use two free actions to call you shot for increased DV and negating armor.
Now, before you try to use the common debunk of what has to immediately follow the call shot action, the actual text is: This action must be immediately followed by a Take Aim, Fire Weapon, Throw Weapon, or Melee Unarmed Attack. Take Aim, Call Shot, Take Aim, Take Aim, Call Shot, Take Aim, Fire Weapon is a perfectly valid list of actions.
You can't call a shot after taking aim without losing the aim effect. Under
Take Aim SR4A 148, "Take Aim actions are cumulative, but the benefits are lost if the character takes any other kind of action—including a Free Action—at any time." So I guess you can technically stack call shots by call shot, take aim, call shot, take aim, eat a sandwich, call shot, take aim xN, shoot and get 3 called shot effects. This is because calling a shot effect's never goes away RAW, just has restricted what you can do following it. Since take aim allows you to "break sequence", you can get out of the call shot requirement.
What are you referencing exactly? The only thing I can find that remotely looks like it might be misinterpreted here is: Additionally, the passengers gain protection from the vehicle’s chassis, adding the Armor of the vehicle to any personal armor the characters are wearing. Called shots may be used to circumvent one armor or the other but not both.
You can't call a shot to negate vehicle armor and personal armor. Personal armor is worn armor, blatantly defined in the sentence, and a rigger cocoon is most certainly not worn armor (it has a barrier rating, is immobile and has that pesky habit of having to be strapped into). I guess you can rule it is, but at that point you might as well just lump vehicle armor and buildings into personal armor as well.
I believe he's counting the rigger cocoon as a second barrier. Now if this falls under vehicle armor, passenger armor, or both for the purposes of called shots, I don't know. I bet you could load this guy down a lot of armor anyways as a way to prevent escape as well and that'll apply.
Right, which would have to be an interior capable of holding vehicle, which would most likely be on the outer edge of the building. Firing through most walls is significantly easier than firing through the transport of doom. Hell low end blast bunkers are only an armor rating of 32. A secure garage is more likely to be in Armored/Reinforced 24 range which is easy as pie for a sniper rifle to penetrate with a decent wielder. If you do the proper planning you can pull it off without a hitch despite the high alert during this time. After all, the high alert is because it is, in fact, easier to pull off during this time.
Generally they're on high alert because there are more people on alert at the endpoint. In transit, they just have whatever they bought along which is going to be on alert. Either way, you're going to have to shoot though a lot of barriers. It's also likely not going to be a good ambush point because whoever built the base would consider snipers sniping at them whereas you can't feasible do that over all of a highway/skyway.
Really the problem is that sniper rifles aren't worth the cost to learn. In situations where you need to pwn something hard, heavy weapons are great and you have a variety of options. If you're ambushing people at a distance, automatics (either though battle rifles or honestly assault rifles) works just as well and have all sorts of non-sniping related uses.
In the one situation where sniper rifles shine, over 600m shooting where you must make sure no one can hear you, you can just default. If you have a high agility score a SR combat type has, you can call shot and still hit. Agility 7 -1 default +2 smartlink -4 call shot and using an image magnification gives you 4 dice and you only need 1 hit to connect (you'll make it 80% of the time or you might be able to buy the hit since you can take your time). Throw a tacnet in there and you have 8 dice which is more than enough (hit 96% of the time).
Y'all are also forgetting the mage part of the equation, so what if the target is inside a rigger cocoon inside an APC? Whip up some spirits and hold one in reserve, send the rest to distract the magical protection, and have the last manifest inside the rigger cocoon with the target. Done.
The reason why you don't do that is because that's what you ought to always do as a mage. Thus a mage sniper is actually just a dude with binoculars and you never really need a gun.