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@count23 When the number of segments in a cylinder is the limiting factor, one option for capping it with a quad sphere is to create a cube then use loop cut to match the number of segments and To Sphere to generate the shape. Scale the new quad sphere to fit then delete any sections that aren't needed or don't line up with the cylinder and use bridge edge loops to join the sphere to the end of the cylinder. The example below shows what this process could look like.

For this particular shape, blending a quad sphere to the open end of the cylinder is a viable option but it does tend to produce a bit more complexity than is necessary. An alternate approach is to use the cylinder's existing geometry to create a hemispherical quadrant.

This can be done by revolving the portion of the cylinder that matches the cut out then extruding and rotating the remaining edge section so it can be scaled up to match the missing curvature. The edge of the non-manifold area can be selected, extruded and rotated into position then connected to the rest of the shape using bridge edge loops.

Below is an example of what this process could look like. All of the geometry here is created and shaped using tools that produce consistent results when lofting or blending edge segments. The final mesh is a bit simpler than a standard quad sphere and most of the edges should already line up with the cut out in the references. Which makes it a lot easier to cut in additional details, without having to manually redirect the loop flow.

There's a number of different ways to approach these kinds of shapes but it's generally considered best practice to rely on tools and primitives to generate accurate geometry. So try to avoid manually extruding and moving individual edge segments to create complex, compound curves.

A lot of air-frame and hull forms are a series of lofted curves so there's always situations where raw primitives won't match. In these cases it can be helpful to keep the base mesh fairly simple and rely on subdivision to smooth out the shapes and add the geometry required to support the smaller details.

@dunnie How does it appear when you sub-divide? Where are the problematic areas? Topology seemingly looks fine, but once it artifacts/pinches, it'll be easier to determine what topology will work.