Any small Software Co., working atmosphere is exactly what you say. Software engineers are educated and at the same time vulnerable. From an HR angle, a weak person cannot deal with them, as from their perspective, HR is a weak issue. They do not bother HR, etc., as long as HR people are friendly with them. If HR goes against any software engineer, they will teach a lesson to HR by not cooperating with their project, ultimately affecting the growth of the profitable concern.
I will tell you one small example: In these small software companies, everything is free for employees because they work to bring profitability. My friend shared this practical example. In one similar small company, the cool drink stocks got emptied the previous day. In the morning, some engineers wanted some cool drinks, and the admin guy said he would organize to get them. By that time, the concerned engineer, along with some other engineers, went to the MD and informed him that there were no cool drink stocks at all. The MD then called the admin guy and started shouting. This is just one example of the scenes that software engineers can create.
In any software company, software engineers are the asset of the company. To start a software business, you only need a place, computers, internet or high bandwidth, engineers, and some US marketing tactics. That's all. The government will provide quick licenses, etc., as you bring in foreign exchange through the company's profit.
On the other hand, if you want to start any kind of manufacturing company, you need a big place, labor, and lots of formalities to get approvals, licenses, where the government is also very strict in sanctioning anything.
So, software companies and their engineers are pets for everybody, including any management. Just leave this issue to the management.
Regarding leave and attendance, just politely talk to the concerned individuals and get it done.
Regards, Ramani