The S60 3rd edition FP1 emulator main pane rectangle, as reported by

TRect r1;
AknLayoutUtils::LayoutMetricsRect(AknLayoutUtils::EMainPane,r1);

does not appear to return the same size rect as a real device.

For example:
Emul - QVGA landscape 320x240 + right S.K reports a size of 320x198 pixels.
A real E61 has a size of 320x200 pixels.

Emul - QVGA landscape 320x240 + bottom S.K reports a size of 320x186 pixels. Worse it reports a rect of 0,27,320,213, but the top title band is only 21 pixels high - so when we create a window based on the info provided by the LayoutMetrics function there is an 6 pixel gap which displays content from app behind (e.g. from the app launcher). Assuming this is simply a bug and should report 0,21,320,213, this makes the size avail 320x192

Firstly we are not very clear why the position of softkeys should be affecting the amount of scn avail to apps within the MainPane... Is this simply a bug in the emul ?

I recall some of this being fixed for S60 3rd MR release.
E.g. In S60 3rd MR
QVGA - landscape 320x240 + right SK - a size of 320x200 is reported = same as a real E61 device.

Yes we fully appreciate scalable UI theory etc, however whilst relatively easy to apply to certain classes of apps, games in particular suffer from this type of variation.
Consider say a Chess board.
If you have 200 pixels high, each board sq can be 25 pix high. Pieces can then be 23x23. By loosing 2 pixels of avaliable screen real estate e.g. to a 320x198 display the board sqs can only be 24x24. Pieces can now only be 22x22 pixels etc.
Background images usually suffer a bit from this as well.

So, is the mainPane size variation simply bugs in the emulator, or is the FP1 emulator truely representative of future devices ??

You may also wish to note that
S60 3rd FP1 emul for 240x320 sized scns reports avail size of 240x235
whereas
S60 3rd MR emul for 240x320 sized scns reports avail size of 240x234