Hello w0lley32, I have worked in the ink and coatings industry for 36 yrs or so and have experienced tiny bubbles forming on patching compound after sealing them with latex primer or even after a top coat with latex or acrylic paints. This may be caused by "off gasing". Because the patching compound on a smooth surface is applied in very thin film it is subject to quick penetration. Components in the patching compound react with resins and or solvents in the latex paints to form gases which bubble up through the surface of the wet paint. Even water base systems have evaporating components. For sure using an oil base Alkyd primer will prevent the bubbling but if you top coat this with a latex or acrylic (water base) paint or primer it may penetrate the alkyd and off gas again. The sure way to prevent this is to top coat with Alkyd paint but it is clear you do not want to use these products so another avenue may be to patch the bubbles with a different type of compond such as Polyfilla that dries much harder than conventional drywall compounds or even white wood filler. I've used both and had good success. You can patch a small area first ,sand and clean and test it for bubbling after you prime with a good latex. For sure you need to find a patching compound that dries with a harder finish to prevent latex penetration and off gasing, otherwise you'll get stuck using Alkyd.

I have had the same problem. usually when putting on a third or fourth coat. Probably from not letting first coats cure enough.

Faron or paintguy may have better input, but here's my 2 cents. Before painting latex over oil, you need to use a primer that can coat oil paint and be top-coated with latex. I believe you'll want to stick to an oil primer for this. Once the stripe of primer has dried, you can cover it with your yellow latex. Personally, I think it'd be easier to stick with spraypaint and use delicate surface painters tape & masking paper to cover the areas you don't want yellow.

I don't know what you mean by lines...are these in the ceiling or the beams and are the lines at seams? The bubbling is certainly not normal and it usually means that there is an adhesion issue. One of the layers underneath is not adhered well in areas and the stress of the new paint is pulling at those suspect areas. It is okay that they sprayed the ceiling instead of rolling it as long as it looks nice.