ffmpeg prores alpha channel not present when colormatrix and colorspace operations are performed
The colorspace and colormatrix filters don't handle alpha pixel formats, so those get stripped off. The workaround is to extract the alpha and then reattach it.

ffmpeg -f image2 -framerate 24.0 -i tif_w_alpha.%3d.tif -filter_complex "[0]colorspace=all=bt709:range=pc:format=yuv444p10:iall='bt601-6-625':irange=pc[main];[0]alphaextract,format=gray10le[alpha];[main][alpha]alphamerge" -c:v prores_ks -profile:v 5 -pix_fmt yuva444p10le -alpha_bits 16 this_has_no_alpha_channel.mov

BTW, The Quicktime specification doesn't accommodate output range pc. Consumers should expect to treat range as always tv. If your software allows to override that, nice, but other software may not.