They are rigged, but not as fully as they were in e.g. Belarus.
Russia is a giant country with 85 "states" and around ~100k polling stations, so the process is very complex and involves different voting and administrative cultures. In some of those states they are fully rigged, with 95% turnout and 98% votes for the ruling party, but in some the elections are surprisingly fair. In a lot of others they can be made fair if any poll watchers are present. Overall the thinking is that they add themselves 10-15% additional votes across the country by straight up voter fraud.
The main way they rig the elections right now is by not allowing anyone who could win to participate and then throwing all of the state resources towards promoting their candidate. That's why consolidated voting for a single opposition candidate can work in this context.
To add to this: this elections are run independently in every region. The government's ability to rig them in one area does not affect the outcome in another.
Yes there is a lot of evidence. From blatent ballot stuffing to more tricks like changing names. This time they even shaved someones head to make them look like the candidate ;)
A concerning development this year is they allow online voting? Which seems like the easiest way for them to flip just enough votes to win, without giving themselves 95% of the votes.
Sometimes they are, but (mostly in large cities) people sign up as election monitors to prevent it. Sadly, most of 90 000 polling stations are not monitored by independent observers.
The main way to control elections now is not letting opposition candidates to get into the ballot. For example, on this elections many candidates were rejected because they are "linked" to Navalny's organisation that was admitted as an extremist organization by the court. Some people are rejected because the signatures they have collected are deemed invalid. Obviously you cannot win if you cannot get into the ballot.
There also is electronic voting (voting over Internet) which is difficult to monitor. It is also worth noting that while you can vote over Internet, you cannot collect more than 50% of required signatures for being added to a ballot this way.
Like turnout percentages have ridiculous percentages of ratios that end in 0 and 5 - as do growth in turnout.