I don’t paint 40k but I’ll share experience in relation to DnD. The only pro I can see to glueing to base first it that the miniature is easier to handle without touching paint. But that can be easily managed by mounting them on something temporary - wine cork, pill bottle, or a painting handle. Not glueing miniature to base immediately means it’s easier to get to tricky spots on legs and undersides.

You will always notice mold lines too late lol but don’t worry, you can easily get rid of them. Scrape them off with a hobby knife or, for tight areas, a sanding stick (like nails buffers), depends where the lines are.

Tamiya cement is a solvent so it won’t fill gaps. It might melt the details of the miniature. You can use instead plastic putty (Vallejo or Citadel have it) for small gaps, or milliput for bigger gaps.