A ballot-counter should be able to identify printed ink against pen ink. If not, I think the consistency of hand-writing would be a little bit of a giveaway. Moreover, you shouldn't have access the ballot paper before the election. If you do, you would need to construct the correct images, trim papers to the right size, etc. in a short period of time previous to the election.

What, you have your own ballot box at home? There should be enough security so that there isn't just one person watching a ballot box at any one time. The whole point of physical ballot-counting is that the records exist in perpetuity AFTER an election, and can't be retrospectively altered without difficulty and physical access.

Moreover, so what if you can swap a single ballot box? A hacker that can hack an entire election is far more dangerous than a loony who has access to a several (at most) ballot boxes. Even assuming some wide-spread fraud, there are enough individuals and ballot-counters involved in the process to identify any such problems, and the physical ballots are kept such that fraud can be retrospectively identified, even if the sources of such fraud cannot.