Stuff that has to be discussed (and should be clarified by WICA): 
- https://wikicarpedia.com/car/The_Wonders_of_Humanity#3._Scoring_a_wonder – If you complete one or more roads that score points during the game – In other words, you do not receive the 3 points bonus from Stonehenge if you complete an unoccupied road, isn't it? But you score this 3 points bonus only if you complete an occupied road, occupied whether by you and/or somebody, whether who has the majority of the road, isn't it?
- https://wikicarpedia.com/car/The_Wonders_of_Humanity#Preparation – To mark your wonder later, we recommend you to take another (marker) meeple in your color. You can also use something else in your color as a marker. – If you use a normal meeple as a marker meeple, can you remove it from the wonder with the festival and use it later to place it on, say, a road? If you use "something else in your color as a marker", you cannot use it later as a normal meeple, isn't it?
- https://wikicarpedia.com/car/The_Wonders_of_Humanity#cite_note-3 – Some wonder tiles include multiple cities spreading across multiple square spaces. Each space should be counted like a separate tile. – A meeple placed on a wonder is not placed on a particular tile. As such, meeples placed on wonders cannot be eaten by the dragon, captured by towers, removed by plague... isn't it?
- https://wikicarpedia.com/car/The_Wonders_of_Humanity#cite_note-3 – Some wonder tiles include multiple cities spreading across multiple square spaces. Each space should be counted like a separate tile. – A meeple placed on a wonder is placed in a special area (like the City of Carcassonne, the City of Leipzig and the Wheel of Fortune). As such, ghosts and the fairy cannot be assigned to meeples placed on wonders, isn't it?
- https://wikicarpedia.com/car/The_Wonders_of_Humanity#cite_note-3 – Some wonder tiles include multiple cities spreading across multiple square spaces. Each space should be counted like a separate tile. – A meeple placed on a wonder is not placed on a particular tile. As such, you cannot move a wagon on a wonder; or use a portal, a flying machine, a "Change position" gift card, a 20th Anniversary "Add a meeple" symbol, or a 20th Anniversary "Place a meeple" symbol" to place a meeple on a wonder, isn't it?
Using a list with automated numbring makes a bit complicated to reply inline, so I'll reply in blocks.
1. No, as per the German rules you only get the bonus for occupied roads.
The wording of the German rules indicate that you need to complete at least one occupied road, it doesn't matter who owns them. If so, you will get the 3 bonus points per occupied completed road. So completing unoccupied roads will not trigger this bonus.
Note: The English rules seem to be mistranslated as they indicate that you need to score some points from the tile placement additionally to completing one or more occupied roads.
2. No, the meeple placed a a marker becomes a token to indicate the player placing the wonder. It is not actually a meeple with a role.
The idea is that the meeple, figure or token placed as a marker on the wonder cannot be removed by any means. It shows the player who placed the wonder and benefits from the wonder. Thay should have provided some cubes, discs or something you cannot relate to a meeple and avoid any ambiguities depending on the piece that you use a a marker. This would be a similar case as removing a scoring meeple from the scoreboard because a catapult Knock Out token fell next to it.
3. Yes, but you have to follow the grid of square spaces.
You always have an underlying grid made out of square spaces. The dragon, the tower, the flying machines... follow the grid to determine their movement, their ranges, their trajectories.... the same as with German castles. A meeple placed in a city on a wonder tile will be implicitly located in a square space.
All this will not matter for the dragon or a tower, since the whole wonder tile will be affeced by the dragon as soon it lands on any space the wonder tile occupies (only the player marker on the wonder itself is safe from the dragon). The same will happen with tower ranges: as soon any square space of the wonder tile is in rage from a tower, any meeple on the wondr tile can be captured (the player marker on the wonder itself cannot be captured no matter if you used a meeple or another figure for it)
Flee tokens will have to follow the grid too. But you will have to allow multiple flea tokens to occupy the wonder tile. This would happen with double-sized tiles too for the plague to spread smoothly. As with the dragon, the first flea token places on a wonder tile will remove all the meeples on it. However, the player marker will stay put.
4. Yes, the wonder itself is a special area, but the marker placed on it is not acting as a meeple. (It could be a token similar to a tollhouse, but HiG didn't provide it

)
Therefore, even if you use a meeple as a player marker on a wonder, no ghosts or the fairy can be assigned to it.
5. Yes, you can use all those mechanics if you follow the grid.
You can do all of this if you stick to the grid. We are just extrapolating from the clarifications given for 1x2 and 2x2 tiles.