I don't think they were necessarily saying the new or slower players have to backtrack... that wouldn't really be the proper words to use. Essentially, it would be kind of like what you suggested. The players who have the newest and shiniest relic going into 3.0 would be able to keep the customized stats on their relics. Those who are still on Novus, Nexus or Zodiac (which will be outdated as soon as 2.5/2.51 comes out) could either trade in their current relic for an upgraded relic weapon with no stat customizations, or complete quests that have been made easier to finish their relic to the point coming out in 2.5/2.51, and then maybe continue it on the same quest line as the 3.0 relic, but with the customized stats. New players or new players to be aren't being punished at all really, they simply have a choice, either do the relic quest line from 2.0-2.5/2.51 made easier, or just skip all that and get a relic weapon from the 3.0 without the customized stats, just the stats in the base line ilvl 80 relic, only buffed up to be on par with the ilvl the new relic begins at.
This isn't punishment, it's choices. Either spend time to customize, or skip that and take what you're given. Either way, you have the new relic weapon, just the people who would like to feel that their time, gil, and effort weren't just a waste would get their wish. Also, your suggestion is quite viable and good too. Just trade in your current relic for a material, or maybe a scroll, or book, or some other meaningless medium with no real rhyme or reason, which will alter the 3.0 relic's stats to those of your 2.5/2.51 relic weapon, and make those stats 3.0 equivalent. In essence, just continuing what has already been worked on so hard. So yeah, both of your suggestions were really the same, only you kind of just got hung up on the punishment part. In the end, it's really the same results with the same effect. I don't think Axe was suggesting that they do away entirely with the 2.0-2.5/2.51 relic line, just that they give the option of either taking the easy way out, or putting in some work (much less work than what players who already have Zodiac have put in) to be able to customize your relic weapon.