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The Chidah in Shu"t Chaim Sha'al 1:71:2 brings down that if one is sitting and holding a sefer Torah and a Rebbe passes by one should not get up. Also, I believe if one sits with a Torah during hakafos it is fine.

When the sefer torah is lifted from the bimah the tzibbur has to stand Sources: Refer to Rashba 3:281, Radavz 6:shnei alofim 16:page 39, Elya Rabbah 149:1, Shach Y.D. 242:38, Shar Ha'tzyion 146:18, Sharei Ephraim 10:18, Sharei Chaim 10:19, Be'er Moshe 3:23:2, Yalkut Yosef 2:134:16, Yisroel B'mamadam 25:63, see Magen Avraham end of 141. One should ...

It's generally considered respectful for the congregation to stand whenever the Torah is out but not "at rest." When it's sitting on the bima; when it's being held by someone seated (e.g. during the haftorah reading); and when it's in the Aron are all situations where it's "at rest." When it's being picked up it's not "at rest", so it's appropriate to ...