Actually we knew all about this - it's not like this move was unanticipated, by us or Microsoft - and the reason we never said much about it is that just as with SSDs, pretty much nothing stops working and there's nothing anyone actually really needs to do.
Support for this was put in place with Vista; it's that OS which broke with the long-established convention in PC operating systems that filesystem partitions should be cylinder-aligned, and by default uses partition table layouts where partitions are aligned on 1Mb boundaries. The system wasn't aware of the sector size of the drives in question, Microsoft just unilaterally changed the rules for partition layout, and much of the work done in Ghost itself for GSS 2.0 involved honouring that layout set by the OS in the source image (that and finding and removing all the places where over the years, cylinder-alignment was an unwritten assumption in the code so that things broke when processing non-cylinder-aligned data).
Microsoft made this change precisely to anticipate the move to drives that are natively 4k-sector, and so from an engineering perspective once we'd adapted to it we were confident that we'd done everything necessary, and that once vendors actually produced these drives we were confident that was the case. During 2010 my colleage Robert Chester worked with 4k-sectors drives supplied to us as engineering samples from drive manufacturers (and with other drives to validate >2Tb capacities, incidentally) to validate Ghost's handling, and things worked precisely as we had expected.
That alignment switch actually comes from the Vista work done in Ghost Solution Suite 2.0 and really it's there to override Ghost's natural behaviour if for some reason it was to make a mistake in detecting the particular partition alignment factor used in the source image (and lots of the Ghost switches are like that, they exist not to be be used routinely but rather as "in case our logic for detecting this behaviour for you turns out to be insufficient").
The big thing is that 4k drives still work just fine in old systems; in fact, hard drive throughput improves generally so fast over the years that in most cases if you were replace a failed drive in an XP system with a 4k one and do absolutely nothing (leaving it misaligned) it'll not only work fine it'll almost certainly still be faster than the drive it replaced.
Basically, these have actually already been in the market quite a decent while; Western Digital in particular were manufacturing 4k-sector drives for over a year and Toshiba were also doing so. If you're using Vista or Win7 there's almost certainly no need for any Ghost user to do anything, and you're still primarily using Windows XP then it's entirely up to you whether to bother or not.