Filler Stain.
There is a product made specifically for this issue...
As a wood boat restorer, I know the importance of filler stain in filling gaps, cracks and grain prior to varnishing. It will be the preferred material of the gap is not too wide.
At 3/32 you are borderline, but I would be willing to bet that a proper color filler stain, mixed with some wood flour will do the trick.
Here is a link to the Dark Mahogany filler at West Marine:
http://www.westmarine.com/webapp/wc...toreNum=10104&subdeptNum=10296&classNum=10300
Here is a link to the Jamestown Distributing page for the Pettit filler stain witha drop down menu showing all colors available:
http://www.jamestowndistributors.com/userportal/show_product.do?pid=6749
Filling with epoxy is a method I would avoid personally. While it will work mechanically, you get one shot on the color. Once it is in, it is in. ALso, an epoxy fill repair will be a lot harder than the surrounding teak material and will leave you with a raised spot if you are not extremely careful with scraping and sanding. Any method you use to try to flatten the epoxy will also work the adjacent wood, resulting in a raised epoxy ridge and a corresponding teak valley on either side.
I will not finish brightwork on any boat, sail or otherwise without filler stain. It is to me a necessary step.
For this situation, and knowing you plan on varnishing, (Cetol) all of the hatch boards, I personally would mix up some wood flour and filler stain and use it as a pre-colored filler. Once dried, I would be comfortable sanding flat with the surrounding teak, as it will be slightly softer. I would then use the filler stain alone to get a uniform stain coating for all of your hatch boards, and then use the Cetol process as described in your link. I really like Cetol, by the way...
These would be my recommendations for a repair that will be easiest to implement, will provide a uniform color prior to applying Cetol, and will also give you a flatter sealed surface to finish. The filled and stained boards will be less porous prior to application of Cetol, providing a smoother flatter finish with fewer finish coats.