A viable explanation offers Maxim Katz (Russian politician in exile) in his recent video (https://www.youtube.com/watch?v=XewD7Qifnck - in Russian, human-made EN subtitles)
In essence, the whole reelection machine at some point switched from "do whatever it takes to get Putin overwhelmingly reelected or face a new president unfriendly to all ex-president appointees" to "He will be reelected, this is a stupid formality anyway, do whatever it takes to impress Him because this is what determines your personal success afterwards".
This explains a lot of less than logical decisions - e.g. using signature collection to back Putin's nomination instead of other, less impressive options.
Collecting 100k signatures in order to nominate a president candidate is bound by prohibitively complex and likely to fail procedure (at most 2500 of them are counted from each region, the timeframe is rather restrictive and a great deal of personal data are recorded in the process, the signatures are counted and verified by the president administration, etc, etc...). It is expected that no one would really try.
On the other hand, a pretty much unexpected result of this procedure is a great deal of visibility, should one really tries - e.g. long (spanning few buildings worth of sidewalk), slow moving queues of pretty much determined people and the process going well into the night, for ~2 weeks.
This is nothing like a sane reelection campaign planner would allow in the first place.
And once the big, visible number of people queued on the streets of multiple cities, the system is pretty much unable to react by its usual toolset. In IT security, this is called a "distributed denial of service attack".
The police in a Russia is pretty much able to deal with a big protest (even tens of thousand people) in a single city. Or even in Moscow and St. Petersbourg at once. Or deal with small number of known organizers well before the event materializes.
100 groups of previously unrelated people all over the country is well above their administrative bandwidth. A less clever manager, of course, can always order the police to beat the hell out of these people wherever they are, but the status quo is rather fragile and a forceful attempt is highly likely to backfire.
This is why the signature collection will be allowed to go on and "solutions" will be looked for later.