Any manufacturer will do the same. As long as the soldermask is wrong, all via are "tented" by default. This is specifically mentionned by all pcb manufacturers (and it's a necessity if you don't want shorts between vias and pads during a reflow process). It is strictly impossible to have some tenting if the gerber file shows a well defined solderpaste mask.
To avoid this kind of trouble, a "no soldermask" zone and a solderpaste mask should be defined -and designed- for each IC if handsoldering is considered (and probably a large 1.5mm to 2 mm "super via" for the gnd pad soldering when possible)
in this case, you can circumvent the problem with a fiberglass pencil and scratch the tenting and the surrounding area of the lower side. You can also (not recommanded) use a hot air reworking gun and solder your QFN after some pre-tinning the pads on the component side. That's what I call a "a phone repairer tip". Not elegant at all but it works (not always)
ps : using fiberglass pencils is a rather dangerous process. One should wear gloves, protective googles and a mask to avoid breathing small glass particles. The working area should be carefully cleaned after each operation.