Hello, I hope I can offer you some assistance.
You are correct that this engine doesn't have a camshaft drive belt, the camshafts are driven by a chain on both the petrol and diesel engines on a 2000 MY onwards Transit.
With regard to the noise you first need to determine if the noise is engine related or if it is related to vehicle speed. If the noise can be heard when the van is stood still and you rev the engine then this narrows it down to an engine,ancillaries (PAS, alternator, ETC) or transmission related noise. The same is true if the noise becomes louder as the engine speed increases but then quietens down when you change gear until the engine speed becomes higher again.
If it is an engine or transmission related noise then have an assistant rev the engine so the noise is produced and listen for the area the noise is from, check that all the turbo pipework is intact as a split pipe will produce noise as the boost pressure increases with a faster engine speed (turbo diesel).
If the noise is only produced when driving and becomes louder the faster the van goes then you are looking for a driveline fault. By far the most common cause of this kind of noise on Transit is a faulty front wheel bearing, if this is the case you may find that when the noise is evident if you turn the steering wheel slightly the noise may become quieter or louder depending on the load placed on the bearing. Jack the front of the van up and spin each wheel in turn and listen for any rumble/grinding sound, also if possible make sure that there is plenty of material on the front brake pads and that the noise isn't because the pads are worn to the metal.
If the noise is very similar to the noise from the roof rack then this is almost certainly a bearing fault. If you need to replace the wheel bearing then you will need access to a hydraulic press.
Start with trying to narrow down the area of the noise (engine or driveline) and go from there.
Let me know if I can assist any further with this or if you have more questions regarding this and I'll reply to you as soon as I can.
from your description this points to a wheel bearing fault. On this model Transit to replace the discs you need to remove the wheel bearing from the suspension knuckle so it isn't uncommon for a bearing to fail afterwards especially if the correct tools weren't used for removal. As you say the noise was present beforehand it may be that the garage didn't drive the van fast enough to notice or just thought that it was the roof rack making the noise. Also unlike most vehicles when a wheel bearing becomes noisy on the front of a Transit you don't tend to get any excessive play in it so unless the garage spun the wheels when the van had it's wheels off the ground they wouldn't notice this.
When braking or changing direction this alters the load on the wheel bearing so this can have an effect on the noise been produced.
Let me know if I can assist any further.