It's easy to interpret their leading zero to mean "use 5-digit representation of years", when (after Y2K and similar problems) I would've expected a better message to be "don't limit the time points that can be represented".
Maybe they have an additional assumption: that humanity won't ever need to consider years past 99,999 in a Gregorian calendar.
Yet they say things like "Our hope is that at least one of the eight headline languages can be recovered in 1,000 years". Come on, we can read text in almost any language from 1,000 years ago, and they didn't care at all about leaving durable texts. A couple of days ago there was this history about a norwegian carved graffiti from around 1,000 AD in Venetia, still readable. They should aim for 10,000 years.
I think they mean about the medium being readable. Carved graffiti (o paper) is more durable than a CD-R. As this media they're using for the "Very Long-Term Backup" hasn't been fully tested yet (we'll need to wait a thousand years for that), they're hoping it will work, but they aren't still sure.
According to the linked article, Their whole purpose was/is to “think 10,000 years in the future instead of quarterly”, so they only need 5 digits for that goal.
This was the first I'd heard of Long Now, but upon reading the article, I had assumed the leading 0 was representative of the infinite continuum of 0's in-front. But all the repetitive 0's had been slimmed down to one, like :: in IPv6
01998. Please.