Ftresi is correct. The statement: “It helps them become modox. which is not as bad as frei” does imply that it’s bad to be modox although not as bad as frei.
However, it is important to remember that the term “modern orthodox” has many, many meanings, and therefore, it is not necessarily incorrect to refer to modox as “bad” depending on the meaning they are using which would depend on the context.
If modox refers to people who don’t dress Yeshivish, then it would not be appropriate to call it “bad”. But if it refers to people who keep some halachos but not all of them, then it makes sense to say that it is bad but not as bad as frei.
There are a lot of other “in-between” meanings which may fall into a grey category about which it is not clear if it is “bad” or not.
In this case, the meaning would depend on what the people who are helped by Project Makom become after they are helped by Project Makom (or what it is that Project Makom helps them to become).