Hello!

excellent questions! it shows that you're thinking hard about this topic.

1) so up til now, we have been talking about each elements' electron configuration in rather simple "modelistic" terms

so when we try to expand our model to explain electron configurations of huge elements, it begins to break down.

this is when we need to ditch old models and use more complex but more realistic ones to explain the universe.

two such models you will come across is called orbital hybridization and molecular orbital theory.

these theories will help you gain a much more realistic view of electrons.

HOWEVER, they are not required knowledge until you start taking advanced chem classes later on,

which is why i don't cover them in foundational level chem classes, such as gen chem.

so long story short :

there are really cool theories that answer the questions you have

but you don't really need to know them just yet. 

and it's kinda hard to explain it all in like 2 paragraphs.

in fact, you can survive almost all of high school chem just knowing the first 20 elements in the periodic table,

and not worrying about any of the other ones.

so.. hold on to this question until you get to more advanced chem classes!

2) the periodic table shows elements in their 'pure', 'fundamental' state.

this is different from the 'most likely realistic' state they are found in nature.

while it is true alkaline earth metals are often "found in nature" with a +2 charge, 

this means that the element has lost 2 electrons from its original 'pure' state.

we are looking at the aftermath.

imagine watching a commercial or looking at a menu showing a "perfect" image of a hamburger.

when you actually order the burger, you would probably not find it as perfect as the picture, right?

the periodic table is the picture on the menu

the actual element is what's on your plate.

you might argue its false advertising; but think of it like this.

the perfect image on the menu makes it easier to see all the ingredients in the burger.

if you take a picture of a realistic burger, some ingredients might be obscured and not show

and then someone with a food allergy can die because they are allergic to onions, but the picture didn't show it.

weird analogy, but you get my point.

sometimes you want to see clearly what the element is, in its pure form

to predict and find out more about it's chemical properties.

the periodic table allows you to do that.

really good questions, 

hopefully all of which will naturally get answered as you learn more about chemistry.

stick with it for now and keep wondering about these things.

good luck on your studies! :D