Wever recognized the need to hit a target like a rail yard repeatedly to keep out knocked out due to the ease of repair.
I don't see anything in that doctrine calling for relentless restrikes or concentration of focus or anything like that. You can find pretty words similar to Wever's about concentration of effort and the need to strike at industrial and transport targets in manuals written by the USAAC or RAF in the late-1930s and early-1940s. But no concentration of focus or relentless restrikes. Nor did any of those words prevented them from falling into the same targeting trap. Wever is not some air power god, he is only just as human as every other air force general at the time.
What will happen, given that the Luftwaffe is only human and its planners are only human, is that this bomber wing will be hitting one target for a few days and then another target elsewhere for another few days. And so-on. Because of this mayfly attention span, the damage done is totally inadequate to change anything. Barbarossa goes on as per IOTL.
Whether that means hitting it multiple times a week is up for debate, but its not going to be a one off type raid due to the understand in 1935 doctrine that a target like a rail yard requires follow up if you can't knock out a bridge or tunnel to shut things down for an extended period.
Even "multiple times a week" is not adequate enough. We're talking literally once a day, endlessly, with (since we only have a single wing to work with) no time to rest and maintain the planes.
And besides the postulated raids would just be a heavier version of the medium bomber strikes on rail yards meaning the issue won't be not knowing how to handle heavy bombers for a rail strike;
And how well did those work out, hmm?
the Germans demonstrated proficiency with that in France and Poland IOTL and again during OTL Barbarossa.
In tactical close air support, not in strategic bombing or logistical interdiction.
Per the capabilities of the bomber they'd be able to handle 8x 500kg bombs as suggested in the OP of the bombers carrying 4 tons of bombs.
So then we're not talking about the Ju-89 (which could only carry a payload of 1,600 kilograms, or 3 500 kg bombs) but some completely new bomber that the Germans have magicked up without sucking the necessary resources, factory space, machine tools, and personnel from some other part of their air, or ground, or naval force. Okay...
But guess what? That still only gives you a average of slightly less then 1.5 bombs landing on target in a 60 bomber raid.
Eventually of course as you said the Germans would overrun Smolensk, but they'd be able to do a lot of damage to Soviet forces drawing supply/mobilizing via it from June and into late July when it finally fell.
Except for the fact that the Germans will just not be doing enough damage.
Where are those numbers from and what altitude were they flying at against what FLAK and fighter defenses?
US air raids in 1944-45 against both Germany and Japan, British air raids against Germany in 1941, and German air raids against Britain in both 1941 and 1944.
The Germans had different doctrine, like what the USAAF eventually adopted by the end which increase bombs on target, which was letting each bomber make its own run with its own bombsight, rather than just aiming with one bomber and having the rest press release based on that.
German level bombing during the BoB, Blitz and Baby Blitz (that last especially) was not any more accurate than American or British level bombing. During the BoB, German Heinkels regularly completely missed entire airfields and did so while bombing from much lower altitudes than the Americans and British would later use when over the Reich, so clearly that did not make as much of a difference as you claim.