Ja is really hard to rate
I agree that Ja is hard to rate but for completely different reasons than you. To be somewhat brief, while the culture has changed drastically since the inception of rap, standards for tiering rappers haven't changed that much from past traditions imo. The perception of Ja's legacy being rooted in commercial success and girly records instead of critical acclaim rap albums like a Nas prevents most circles from taking a high opinion of his career output seriously.
shyt, I actually got push back in the past for putting Ja on a higher queens rapper tier than Mic Gernimo, Lost boyz, Royal Flush, and Onyx which seems insane to me. It seems you can't rate him high mainly due to superficial factors but at the same time you can't rate an artist with his success and consistency low either which makes it hard for many to find a fair position to place him.
his most stand-out works are his hit singles, featuring perfect female hooks and beautifully mixed production.
I take issue here. I can see the claim that his hit singles are vastly more popular and known, which really isn't that abnormal for any artist especially for a consistent hit-maker. But in terms of his hit singles being the most highly rated work on his albums, i'm just not sure how you reached that conclusion, or at-least i'm not seeing this drastic divide between his album singles and album cuts that I think you're tying to paint? Because most people who I've come across who are familiar with his albums can usually cite multiple non-single cuts as one of their favorites for a given Ja project.
For example, I've never seen anyone say Holla Holla is the best tack on VVV or even one of the best; its usually tracks like Suicide Freestyle, E-Dub & Ja, or Race Against Time that's highly rated and none of those were hit singles. And I would argue the same thing can be seen -- to a lesser degree but still significant -- with his others works too were his singles are the female oriented tracks you're referring too. I can't count the amount of people who rank 6 Feet Underground as either the best track on 3:36 or at-least one of the best. The same can be seen with Dial M for Murder and Pain Is Love.