It's not "significantly lower" but it is lower. It is correct that when the MoD writes "losses" they are referring to the combined number of sanitary (wounded) and irretrievable (dead) losses. But we know from a lot of reporting that for Ukraine that ratio is not good, they are having significant trouble getting medical help to their frontline troops in time and often they just leave them there. So if you just take half of that number from the MoD you already have a reasonable estimate.

You assume that they systematically over-report but the truth is you don't know that, and for all we know there could be systematic under-reporting happening to an even greater degree. A lot of Russian commentators have suggested that the MoD really only reports what can be visually verified as a hit, but there is a lot that happens that can't be directly observed. There are a lot of spotter drones, but not everywhere and seldom for strikes in the rear on logistics and such. And as you say, all of this is before you include losses from non-combat related causes.

So far the MoD numbers have tended to be very reliable, or at least composed according to the best information available to them. Insofar as they have reported on Russian losses they have also tended to agree with the estimates of pro-western organizations like BBC's Mediazona which while biased at least try to have a somewhat decent methodology.

So yes, take any numbers that the MoD puts out with a grain of salt, but at least they are not the inverse opposite of reality like in the case of the nonsense that Ukraine claims.