Hi, it should not matter if the points are far from the base point as it should just make a larger surface. If uou have a few points outside of yhe site you do not wish you could delete those either before or after import.
I may have just had an example of what you mean, the one I just did had a warning like the one you mention and i could not see the solid. however straight after import i clicked edit surface and i could then see the outline and in properties I adjusted the offset from level to 0 and it was all there and visable.
Difficult to work out why from a chat here, maybe take some pictures and explain what you have done on a forum / group for revit users. There should be some people happy to work it out. Include links to files if you are able.