Here is what we did to include our wiki in a package. The idea here is to create a new wiki and include all articles under the new custom wiki. When selecting in the customization you will select the new custom wiki. In My Example I called this "HelpCustom"
Create a new wiki in CONFIGURATION > DOCUMENT MANAGEMENT > MANAGE > WIKI
We added the wiki to the main horizontal bar in the help section. You can define where your wiki lives by selecting the location in 'Site Map Location'.
Find your article in the location you picked in the site map location and add any articles you need.
In your customization project, under Wikis, click Add (+) and select the Wiki created from step 1.
Now the problem you have is how do you transfer the articles to the new wiki so you don't have to redo them. I did a quick test to move an article that was created in a different wiki and here is what I did.
Find the main wiki record in wikipage that you created in step 1 above.
SELECT *
FROM dbo.WikiPage
WHERE [CompanyID] = 2
AND [Name] = 'HelpCustom';
Use the PageID value from the result above as the WikiID and ParentUID in your articles. If you need the articles nested then you will have to adjust the ParentUID to fit (or leave the value as is depending on the row not being at the root of the wiki article tree). I would assume you only need to change the ParentUID value for the top level articles. Otherwise just update WikiID for all articles that need to move.
Here is the script I executed. I could not tell if I needed to update the [Number] column value or not.
UPDATE dbo.WikiPage
SET [ParentUID] = 'F1BF807E-4B0E-414C-B90B-83944AC66D8C', /*Use PageID from parent*/
[WikiID] = 'F1BF807E-4B0E-414C-B90B-83944AC66D8C' /*Use PageID from main wiki*/
WHERE [CompanyID] = 2
AND [Name] = 'TESTDEV1'; /*article name*/
I had to restart/refresh my site to see the article move to my new wiki.
Hope this gives you some direction.