Metaplasia may carry some risks, but does it necessarily prevent the esophagus/stomach from functioning properly--prevent either from doing its job?

It does not: Apart from some forms being an occasional breeding ground for malignancy, it's harmless.

No: Intestinal/gastric metaplasia of distal esophagus means replacement of the squamous epithelium with glandular (Barrett's esophagus) and is often associated with gastro-esophageal reflux disease (regurgitation of gastric acid into the esophagus which causes "acid burn" (heartburn) and inflammation. If the latter is severe, it may interfere with the entire digestive activity