The US government has given Bowker a sort of protected monopoly on ISBNs, so Bowker is the only authorized top-level distributor of ISBNs in the US.
Some companies have negotiated redistribution rights with Bowker, so they buy ISBNs in bulk and resell them at prices lower than what Bowker charges for their self-publishing packages. For example, Amazon Createspace sells a single ISBN to publishers who use their platform at a lower price than Bowker would charge for a single number.
It looks like the site you linked to is buying ISBNs under the imprint name of "Independent Publisher" and reselling them. Here are a few things to consider:
- When you buy from Bowker you control your ISBN record directly and can make changes by yourself if necessary. If you buy from a reseller, you will have to request that they make changes for you and trust them to follow through.
- When you buy from Bowker you can use your company name as the imprint name, if that matters to you. If you buy from a reseller, their imprint name will be listed on the record, whatever that may be ("Independent Publisher" in this case).
The reseller you linked to is being a bit deceptive in their wording. The recommendation is that you use a separate ISBN for each format, not each platform. So EPUB needs a different number from MOBI/KF8, and PDF needs yet another number, but your EPUB can use the same ISBN on iBooks, Nook, Kobo, etc.
Giving your ebook an ISBN allows distributors to report sales statistics about your ebook to industry lists. I'm not aware of much other practical benefit that an ISBN provides, as none of the major distribution channels require them. Personally, I currently only use ISBNs on print books.