Is "manifold" as meaning "rightfully so-called for many reasons" used only with pejoratives?

My own recollection is not dissimilar to your own. I believe it is widely used pejoratively.

However if you look in the OED, among the "manifold senses" given of the word "manifold", they cover all sorts of circumstances. I have not included below anything prior to about 1870.

Sense 1a

1892 A. Conan Doyle Adventures Sherlock Holmes viii. 184 I have heard, Mr Holmes, that you can see deeply into the manifold wickedness of the human heart.

1915 W. S. Maugham Of Human Bondage lxxxv. 447 More green than jade brought by swart mariners from the manifold, inexplicable China.

1990 E. Kraft Reservations Recommended iv. 157 The manifold illumination of the city..picks out details at random.

Sense 2.

1880 A. Geikie Elem. Lessons Physical Geogr. ii. x. 67 It is from this circulation of water that all the manifold phenomena of clouds, rain, snow, rivers, glaciers, and lakes arise.

1925 J. M. Murry Keats & Shakespeare ii. 23 One could go on trying to capture all the manifold implications of that line for ever.

1954 O. Sitwell Four Continents ii. 46 The Bowes Museum is vast, its exhibits are manifold.

1986 M. Foot Loyalists & Loners 60 The ramifications of this passage..are so wondrous and manifold that it would be tempting to devote a whole thesis to it.

Many further senses are listed.