The thing about the relationship between Will and Lonnie is that it sucks in its own unique way, distinct from the ways that the relationships Lonnie has with his ex-wife and older son respectively damage them, but I also think they're strangers.
Will does not get Lonnie at all. He doesn't really know what Lonnie wants or what he's looking for or what motivates him. He can't anticipate what he'll do or why. He thinks there's some way to please him, but it doesn't exist. Lonnie is confusing and probably stressful, and dealing with him involves some degree of engaging in a strange game that doesn't net Will very much, but he's looking for the kernels of joy and connection he can scrape from the experience.
It's the implications of his absence that loom over Will, I think, more than his presence. He represents what could have been because he's a big unknown whose sole contribution to Will's life was shame, through implicit rejection and ridicule and lack of interest, back when he was younger.
And I wonder how Joyce addressed that. We know she must have said something and supported him, and if Lonnie spewed any of his bigotry and verbal abuse within Will's earshot and she knew he was aware of it, then she would surely have said something. But she's not perfect, and she can't be everywhere or always say just the right thing, and maybe there isn't always a right thing to say. Maybe she fell back on "you know he doesn't mean it" or "he's wrong and you shouldn't listen to him" or "something came up and he couldn't make it but he's sorry he couldn't take you" or "it's not about you" and that's kind, but doesn't get at the heart of why what he's saying or doing matters, to the extent that it does. And it's not like Will can't tell when she's being untruthful to spare his feelings; he can hear her yelling down the telephone.
But it's a hard line for her to walk as a parent, and so there are gaps where the edges of the white lies and hard truths don't come together neatly. Same for Jonathan, whom we can see trying to make up the difference and reach Will, but who very carefully does not tell Will the whole truth either (that Lonnie does not care and he's wrong even if he's correct and what he thinks doesn't matter); he tells him a different truth that, for him, matters a great deal more, about the world and who Will can be in it.
But, still, those gaps, where well-meaning hands reach with love and can't quite touch... There's a shame that flourishes there, in those dark crevices. And it's very relevant to everything he's got going on, and Lonnie's shadow is definitely there, but Lonnie is just one part of it. Because the only thing he really ever learned about Lonnie was that Lonnie didn't want him and he could never be good enough to change it. I think a larger part of Will's hangups stem from steeping in that town all his life.