With that set of conditions, in my opinion you are definitely NOT self-employed. Look at the checklist that HMRC produces and draw your own conclusions.
http://www.hmrc.gov.uk/employment-status/index .htm
This has far more importance than the toilet breaks - if your employer thinks it is going to treat you as self-employed, it will not pay your employers NI and you will have to pay it out of your own pocket (about 11% or so of your pay).
There's nothing to prevent an employer putting a condition on its employees requiring them to be on time - but that's the least of your concerns - suggest you sort out your employment status.
This does not sound like a great company to work for.