If you're interested in solderability and manufacturability, then you should follow the recommended pad layout. I've never had a manufacturer's recommended pad layout give me grief, although I have run across a few vendors whose dimensioning requires a fair bit of headscratching and pencil-and-paper chicken-scratching in order to figure out offsets and spacing.
You are making some bad assumptions in your calculations though. No, pins are not often centered on the pads "lengthwise" but they are often centered widthwise. Y1 and C1 would most certainly be given by the manufacturer. The recommended land pattern will (in my experience) give more space for the pin on the "outside" of the pad and less underneath it. My guess is that that gives a good shape to the solder connection. You won't have anything in terms of heat dissipation unless there are a lot of grounds or you have a ground pad underneath. In the case of a lot of ground pins, you'll want to give them a lot of copper fairly quickly, but you'll want to connect the pad to the copper with thermals or you'll have soldering problems.
I wouldn't worry about minimizing board space, especially if you're not building a million of these. The half a millimeter you might save by shaving Y1 a little isn't worth it.
The board, pad, paste, insulation, second layer of paste and component in this case must be as close together as possible, really tight together, but you should be able to use it fine provided the pad is large enough to dissipate an adequate amount of heat.
Typically, if the pad size exceeds the component size, you can use a high temperature iron (400C+) and a generous amount of solder to 'tin' the pad until there is a thin layer of solder on it, then you place the legs of the chip down firmly and reheat the solder until it takes onto the underside of the chip.
You will know that it's done when a fillet is formed in the small gap that is left behind when you place the component on the solder layer, seen closely from the side under light.
Either way, just make sure you have very good contact. Solder makes the 'best' contact, paste is kind of terrible in comparison, but still very good compared to nothing at all.
In any event, make sure the heatsink and its pad on your board are isolated from everything else, unless it happens to be the case that the heatsink on your component isn't connected to anything.
Best Answer
I don't know if there's other ways to do it, but the ground pad is going to end up being a pin of some sort. You could try drawing something in the module editor that suggests a pad, but in the end it comes down to pins. Make a pin on the schematic part and call it (the pin number) "PAD". Similarly, call/number the ground pad on the footprint "PAD". Then if you link PAD to ground on the schematic, the connection will get into the netlist. You also might want to add some text in the schematic about the thermal pad.