Usually no matter what device I find when I go to put in the batteries it says to put them in head to toe so to speak
For instance I’ll draw a crude drawing
+{=======}-
-{=======}+
I never thought about it much till I found an old beat up walkman for tapes
the arangement was
-{=======}+ -{=======}+
So the question is does it really make a difference? Could they design the device to work liie
+{=======}-
+{=======}-
Sure, but since you want to connect the ‘+’ of one battery to the ‘-’ of the other it makes sense to arrange the batteries so those two are close to each other.
Drawing one is drawing two bent in two. 
I reverse the batteries in my rotisseries so that it turns the goose in the proper direction.
Oops maybe this should be posted in the BBQ Pit ?
The arangement of batteries side by side, with polarities reversed is mediated by a small strip of metal at one end that connects the two 1.5 v batteries, to make the equilvenet of a 3 volt “battery”. It would be the same as puting them in a line so that the ends line up, electrically.
FML
And you could still do that, with batteries arranged like in your third drawing. But it would a wire connecting the back of the top one to the front of the bottom battery, and then (probably) a connection from the back of the bottom one up to near the front of the top battery, so you have both power leads available to the equipment. So you would have 2 connections in an X form for this arrangement.
That would be more complicated, more prone to failure, and (most important) more expensive to manufacture than the current arrangement. But it would not make the equipment run any better. So there is no reason for a manufacturer to do it this way.
And to add to that, putting them in without the polarities reversed (so your ‘battery’ is - + + - or + - - +) will result in a net charge of zero
By the way, does doing that hurt anything? My daughter LOVES remotes so when she’s playing with them I usually flip one of the batteries around so it doesn’t change the channel, but I don’t lose the battery.
To the OP: Your last ascii art drawing shows the cells in what is known as a parallel connection. This can be done for higher current capacity, but in general is not a good idea. The only remotely mainstream application I can think of is the starting batteries for model airplane engines: The Cox brand batteries had 4 paralleled D cells inside a cardboard Shell, and I used to make my own batteries using as many as 8 D cells…this was far cheaper than the single #6 cell that was the alternative.
The problem is that a stronger cell will try to charge any weaker cells. This is not too bad if you start with new batteries from the same lot, and they are normal carbon zinc dry cells, which have high internal resistance, that serves to somewhat balance them.
Low internal resistance cells, like NiCads, and NiMH, are a different kettle of fish. I would go so far as to say that paralleling such is outright dangerous.
As you have noted the voltage (well you said charge, which is not correct) is zero, but only if the two cells were exactly equal. They will never be exactly equal, so the voltage will be the difference, which has a 50/50 chance of being the wrong polarity.
That said, below about 0.5 V most electronics will not be damaged by reverse polarity, so the battery voltages would need to be mismatched by a LOT. That might be the case with one new cell and one depleted. It is not likely with low voltage items like a remote, but designers often include a diode to protect circuits against polarity reversal…this wastes about 0.3V though, so as I said, is rare in low voltage circuits.
Not necessarily. The battery compartment could have a long wire connecting the positive end of one battery to the negative end of the other, i.e. connecting them in series.
However I do own an alarm clock which has two AA betteries side by side, and connected in parallel. I know they’re connected in parallel because the clock works fine with just one battery.