It has been noted that our players might be at something of an advantage by the time they arrive at Farshore, due to a severe limit on magic to purchased or ordered from NPC craftsmen(due to the limited levels available).
A few possible ways to get around this...
1) Farshore does have spellcasters capable of casting spells of up to third level so you can make potions and scrolls to that level available. Specialists also exist that can produce quality items suitable for enchantment, certainly anything made of leather.;)
2) Increasing the level of the NPC specialists is not to hard to justify. When the Jade Ravens go off on one or more missions of their own, have the local priest(6rh level) or mage(5th level) accompany them without mentioning it to the party. For all we know the cleric is only a few hundred experience from his next level.
Imagine their surprise when 4th level scrolls and potions are suddenly on the market!
3) Olman resources. No reason that the Olmans can't have the ability to create the incidental magic item, especially if the party can provide some service or equipment that they need in return. Since every village reportedly includes a 'zombie master', if we assume they can create the undead we assume a median level of spell casting in each of the seven villages.
4) Let the party develop their own skills. On the negative side it does have the unfortunate side effect of reducing the skill points of at least some party members. On the positive side, a few complaints about 1st level characters going to level 20 in a single year have come up so you can extend the time simply by giving the party greater down time.
I'm going to assume you have a typo in your first sentance, and meant "disadvantage" rather than "advantage", as the body of your post implies.
Overall, I agree. In my game, I changed Professor Aldwattle to an Expert 2/Artificer 5, who after being saved by the PCs is both willing to adventure with them for only his fair share of loot, and to "reserve" half of his Artificer craft points (the phantom XP for item creation) for them if they provide the materials (GP and such).
Other suggestions/notes. The idea of special components is not without note. Consider the T-Rex Temuahti-Tecuani; his hide is abysmally thick. Perhaps Hide armor made from it readily accepts the invunerable property, say at 75% the normal cost to make? Considering the other legendary monsters specific physiologies, you could find some other interesting corellations. Ceratakatha's stinger made into a heavy war pick, with enchantments similar to the dagger of venom?
Olman Zombie masters are at least 5th level clerics, so its totally legit that they might have crafting capabilities in their own right. Also consider that druid is also a totally reasonable class, and many of the "cooler" magic items/properties require spells that druids have access to sooner than clerics: shocking, flaming, etc.
And it has been noted that there is no reason to not let the party take some heavy down time. The campaign's timeline is not "on the clock" after the conclusion of ToD, so PCs can dither away at projects, go adventure, dither, adventure, and such as they like until either they or you decide to advance the story by moving into the next Arc.
I have strongly suggested that craft and proffession skills should be taken as well as covering many of the knowledge skills within the party. As a fan of the item creation feats though I thought about crafting a 'lab' for potions on the Wyvern. I think a forge would be hard to come by onboard*, but PCs will need something to do over the course of a six month sea trip. They should be able to even craft some masterwork items (for later magicing).
*maybe not since it is fantasy, protection from fire cast on the deck?
Craft skills and item creation feats should be major part of the "non-adventure" portion of any campaign. Ditto with roleplaying the "purchase" of magic items. IMO, only those items with a market value of up to 8,000-10,000 should normally be available for open sale. Anything more must either be commisioned or traced to an owner and bought/stolen/traded for/won.
You may also want to work in affiliation/political maneuvering or training (DMG pg. 197-198). In short, just because the characters aren't adventuring, doesn't mean they're inactive.