It sounds like your employer needs this to calculate the correct reimbursement of travel expenses for this business trip. Czech labour law lays out a notoriously complex set of rules on how to do that. (See for example this nice writeup in Czech.) In short, your employer has to pay you a fixed daily meal allowance (a.k.a. per diem) according to a country-specific rate set by the law (e.g. €50 for Germany). For each day of your trip, the country in which you spend the most time determines the applicable rate, and this is what you need the border crossing times for.
Article 154 of the Czech Labour Code specifies that time spent abroad is determined from the time of border crossing as reported to the employer by the employee. In case of flights, what matters is the departure time on the way out and the arrival time on the return journey:
Dobou rozhodnou pro vznik práva zaměstnance na náhradu cestovních výdajů v cizí měně je doba přechodu státní hranice České republiky, kterou oznámí zaměstnanec zaměstnavateli, nebo doba odletu z České republiky a příletu do České republiky při letecké přepravě.
You can notice there's no notion of "scheduled time" in that paragraph, so strictly speaking these should be actual border crossing times, including delays and the like. However, opinions vary on how strictly to apply this in practice. The general consensus seems to be that it would be unreasonable for the employee to have to watch out for border posts and record the exact time they passed them, so unless you're travelling by car, you will typically be expected to report some officially listed border crossing time for your train or bus.
Many companies do as far as to disregard any delays altogether and insist on reporting crossing times exactly as they are in the timetable (even though this has no real support in the law). That's mostly because such companies don't trust their employees, so they want some sort of a "paper trail" instead. (As in, "we don't care your flight was three hours late, your boarding pass clearly says you departed at 12:00". Sadly, such an approach is disturbingly common among Czech employers.) Mainly bigger corporations also want you to report planned border crossing times for internal budgeting reasons (so they can pre-calculate the expected costs for your trip).
As far as international trains are concerned, there's always a specific border crossing point listed in the schedule with a particular time, and this is what most Czech employers expect you to report. You might have to use for example the Czech idos.cz trip planner to see this information. A random example (yes, it is always in Czech even if you switch the website to English):
Finally, remember you typically don't need to worry much about accuracy. The only thing that matters is
- which foreign country you spend the most time in in any given day
- when only a part of a day is spent abroad, there are four bands for the meal allowance with cutoffs of 1/12/18 total hours abroad
So unless your itinerary puts you close to one of these boundaries, it doesn't matter at all whether you cross the border an hour earlier or later as the overall outcome won't be affected.