When is a sub-optimal Pokémon better?

It depends on the IV distribution, but the difference between 90% and 100% mon is pretty minuscule in general and unlikely to matter often.

Lvl 40 mons against lvl 40 ZH/DG Blissey:
Machamp 11/15/15 Time to win 51.6s, power 94.7%
Blaziken 100% Time to win 54.6s, power 83.4%
Machamp 9/10/10 Time to win 51.7s, power 84.1%

So Machamp can be way below what most people consider acceptable IVs for maxing and still come out ahead of Blaziken. This will always depend on the matchup, 15a Blaziken will reach Counter breakpoints sooner than Machamp, which will result in a big boost when it crosses the breakpoint but Machamp doesn't.

Hariyama and Breloom don't have an exact point where they become better than Machamp due to their stat distributions. Against the level 40 Blissey, level 40 Hariyama deals about the same DPS as a a level 20 Machamp while its TDO is somewhere between level 30 and level 40 Machamp. Level 40 Breloom will deal almost as much DPS as level 40 Machamp but its TDO is a bit below level 30 Machamp.
EDIT: Pokebattler was lagging and I looked at wrong movesets by accident. L40 Hariyama actually has more power than L40 Machamp and is only a bit behind in DPS against L40 Blissey.

Leveling up higher can absolutely make the #2 mon surpass the #1 mon. Sceptile is very close to Exeggutor in DPS and will surpass pretty easily if leveled higher. Venusaur is tankier than Eggy but further from the DPS so catching up is harder.

I can say something about the grasses:
In Pokebattler sims against Omastar my lv30 Venusaur is about equal to my lv30 Eggy (if I TM'd the latter to BS) and a lv30 Sceptile would perform more or less the same as them. Lv33 Vileplume and lv 34 Victreebel (weather boosted wild catches) are a bit behind but could still be a part of a comfortably winning team (both have a time to win of ~164s).

Against Vaporeon only the Eggy and Sceptile would have had viable times to win (174s and 177s respectively) though both are cutting it close. Venusaur is the closest to them at 179,9s and if it reaches a breakpoint within a couple of power ups I think it would be about equal to the two.

Tl;dr
Venusaur and Sceptile are really close to Eggy already at the same level. I'd say that Vileplume and Victreebel at lv35 (wild caught) would be a bit behind a lv30 Eggy but not by much.

Simple answer is Yes. There is a opportunity for Blazkin to out DPS Machamp at lvl 40 with 15 attack stat but only during the weather boost. On other weather days Machamp will out perform but if you have a Blazkin on a cloudy day at lvl 40 15 attack stat vs Tyranitar he will do 20 dmg per hit!! vs Machamp who can only do 19. Is this worth the investment? that is up to you.
Source: https://goo.gl/mhYfmz

It also depends on the situation. Both Machamp and Blaziken will perform badly against fairies, flyers, or psychics. It only makes sense to ask this question in a context. Against the usual foes for Machamp, how will Blaziken fare?

Against Ttar with Iron Tail and Fire Blast, I'd think Blaziken with Counter/Focus Blast might have an edge. Against Ttar with Bite/Stone Edge, Machamp clearly wins. Against Snorlax/Blissey/Chancey, I'd give the edge to Machamp unless Blaziken is a lot better.

For the example you give, I suspect that 5 levels and the 10% edge in IVs would make Blaziken comparable, assuming no typing differences in the matchups. But I do know that in raids, when I choose a "Supreme" matchup with a lower CP, it doesn't perform as well as a "Good" matchup with a better CP. One example is Poliwrath vs. Ttar - I have a couple, and they do all right, but I feel they don't carry their weight in terms of doing damage in the fight because of their lower CP. Would rather use a RS/EQ Rhydon with almost 1000 higher CP, because it does more and takes more than the better typed (for this fight) Poliwrath.

We'll see how it all plays out, and of course, as the meta shifts, something may gain or lose relevance at any time. It's really fun when "that useless thing that I just couldn't throw away" suddenly becomes just the thing. Like when my Lick/Earthquake Snorlax became a good tank for Gengar raids. So don't bet it all on one horse, spread your investments around to better manage a changing landscape.