At GrantTree we use Workable - and I find that it's fantastic as an ATS. Full of features, great integration with Gmail and Google Calendar (e.g. we have Chrome Boxes in our meeting rooms which create meeting room calendars, and Workable allows us to book the rooms when we send calendar invites for interviews).
For our HR software (for booking leave, basically) we use TeamSeer, and we get free access to it (and are required to use it!) with our long-term sick leave insurance policy. It's lightweight and easy to use. But, as you say, it automatically assumes that you have a 'line manager'.
Well our solution with all of these things is to hack them. Generally with any software tool we use, we make every user an Admin unless there's a reason that would cause harm. We also tend to be transparent about everything, and share information with everyone that we possibly can.
On the HR software, I just make everyone their own line manager. This means that when they get back from sick leave, they have to fill in a form to confirm why they were off (the insurers require this), and then they have to "approve" that form as their own "manager". (It then also automatically emails me, because the system has to have a designated "HR Manager" - and I just have an email filter set up to delete those mails automatically). It's also possible to set it so that people can approve their own holiday without needing manager approval - and you can have multiple groups, so you can have everyone in one group, and then sub-groups available too.
I think that's how it always has to be - you hack the system to make it work for you. (Hey -it's like Holacracy, right? Any set of tools you get off the shelf is not going to fit you perfectly, so you use some bits a lot, and others not so much, and you hack it to do what you need it to do).
IT's frustrating that the rest of the world assumes some things about how companies work and how working relationships are that you don't subscribe to. Welcome to the world of being queer! Time to start campaigning for the business equivalent of gay marriage!
Best wishes, Andrew