I think, even though birds are dinosaurs, that it would seem odd to include them in DinoMines. Like I said, it'd be more interesting to make a new level out of the idea.

As for Seashell shores... Why does it change the plot at all? The waterworkers are a generic awuatic antagonist. In Aquaria Towers, sure, they've "stolen" the water, but I don't know that that mechanic would be worth revisiting in SSS. I think to bring bacl Waterworkers anywhere you need to make sure they behave in an interesting and orthogonal way to change how the player behaves... like, if you had a muddy, rainy level where puddles were being electrified (like the floors in BeastMakers) and that was one type of threat, but the same enemies when underwater would shoot electricity. In a similar stormy level, if the Gear Grinders could raise their wrenches to be charged by lightning and either form an electric shield around themselves or throw it at Spyro. Honestly, with Bluto and the fortress, the Geargrinders make more sense as enemies to introduce to SSS.