Also, once the cylinder is raised or lowered to alter the port timing by the means of changing the thickness of the base spacer/gasket, the squish hence the compression is also changed, so this must be adjusted accordingly to compensate.
Several factors must be looked at all at the same time once u start playing with the ports - even the intricate details such as the individual radius at the various parts of the exhaust port - these are the little yet very important details that are taken into account when calculating the exact shape when blueprinting a custom pipe to suit a specific port design. Also, the top and bottom edges of the ports can not be at an absolute horizontal as this would catch the rings and cause severe damage.
Man I'm sorry but just have to interject here as I hate seeing info like this when people are trying to learn stuff here, misinformation helps no one and just makes things more confusing than need be!
Raising the cylinder or lowering it with gasket thickness is common practice for helping in correcting squish along with decking when needed, the thickness of a couple gaskets is minimal in it's effect on the timing because each mm of sweep is 4.3-4.5 degrees mathematically but in actuality it's less than that due to dwell in the top and bottom.
This amount of degree change is equal in all the ports since your raising or lowering the whole cylinder not individual port's and this means the durations stay the same, blow down stay's the same and so on it's just slightly shifted the opening degree's and not enough to make much difference tbh.
Pipe design requires knowing the exh port timing and the peak rpm with the outlet/flange dia it has very little to do with the exh port's shape, the header dia and length along with the first cone's volume and angle are what pull out the gasses from the cylinder and the second cone's volume and angle determine the magnitude and volume of the return wave.
The exh port's shape at the window or cylinder wall needs the appropriate cross section just after open most importantly and the shape below that is irrelevant at this point and only at bdc and up during the return wave will this lower area be in effect and flat floor's are very common on all ports with proper chamfered edge's they will not snag the rings and there is a reason for this on the exh port in small displacement 2t's.
If the pistons crown does not come down flush with the ports floor at bdc which many don't, there is a slight ramp in the tracks floor to help deflect the return wave up over the exposed edge of piston and the dome into the chamber.
Many top builders will ensure that the crown is flush at bdc and then deck accordingly but rounding this floor has no point and will reduce the cylinder fill from the return wave due to eddy current's caused by doing so! here is a typical performance ported 2t it port floors are all flat!