The "extra" space is there to accomodate the border of each unit frame. If the frames were flush up against each other "at rest" then when a status on the frame border was activated, they would overlap.

Yep, spacing is the setting you want, not padding.

Spacing controls the amount of space between each individual unit frame.

Padding controls the amount of space between the whole group of unit frames and the edges of the backround frame. Think of the backround frame as a box, and the unit frame are its contents. Like packing peanuts a real box, padding is what goes in between the boundaries of the box and its contents. Note that if you've hidden the background frame (by setting the opacity of its background and border colors) then the padding setting has no real visible effect.

This has been asked and answered dozens of times over the years. Grid relies heavily on Blizzard's secure group templates, which do not provide any way to generate frames without having actual units in an actual group. The authors of Grid, myself included, have always felt that adding the amount of code that would be required to manually generate fake frames is not worth the marginal convenience it would provide to some people.

If someone else wanted to write a third-party addon/plugin that hooked into Grid to provide fake frames for configuration, nobody would stand in their way.

Personally, I’ve never found it remotely difficult to roughly configure Grid while solo, and make small tweaks as needed while in a raid. There’s always downtime in a raid, while people drink between pulls, or distribute loot after a boss kill, or just take a 5-minute break. If you’ve taken a few minutes outside of a raid to familiarize yourself with Grid’s menus, it only takes a few seconds to make any change you can think of.

Remember, you don’t have to use “real” settings for configuration. For example, as a mage you can apply Arcane Intellect at any time; if you need to check the size of the center icon, cast Arcane Intellect on yourself, add Arcane Intellect as a buff in the auras menu, and enable Arcane Intellect on the center icon indicator. Once you’re satisfied with the way the center icon looks, disable Arcane Intellect for that indicator, and delete the buff from the auras menu if you want.

If that isn’t good enough for you, you can always invite random people from your guild while they’re doing dailies, or hang out in Alterac Valley.

Read the tooltip that appears when you move the mouse cursor over the minimap icon (or DataBroker plugin). You should see this:

If you don't see the first line, you should completely delete it and reinstall it from a fresh download, as you are missing the embedded library Grid needs to provide a GUI for configuration.

Your other option is to type "/grid" and use the command-line interface.

There is at least one plugin that provides this functionality.

Mana bars are provided by a third-party plugin, which I cannot provide support for.

Personally, I believe mana bars are counter to the basic design intent of Grid, and are a waste of screen space and system resources. Most of the time it does not matter how much mana someone has; with mana bars, the information is always there taking up space and adding clutter to the frames whether you need it or not. In any given situation, you will be better served by either the percent-based Low Mana status (eg. if you're a resto shaman, use the status to show when someone is below 76% mana and can fully benefit from Mana Tide) or a plugin that activates a status at a certain fixed value (eg. in the Kaz'rogal encounter, if someone drops below 2000 mana they explode). Conditional statuses are more effective than a traditional bar; they provide more precise information, and they only occupy space and attention when the information is needed.