Kyoto’s Prepaid travel card

Surutto Kansia Miyako Card's value starts at 1000. The flatrate bus fare is 220. It doesn't round off. So what happens if I bought the 1000 value prepaid card and travelling on my 5th bus (thus my prepaid balance is only 120)? Am I allowed to top up with 100 cash upon getting off the bus?
Secondly, the Traffica Kyoto Card is of better value as there is a discount (unlike the Surutto), but it is not as extensive as the Surutto Kansai Miyako Card, right?

In response to the second question, the Traffica Kyoto Card is discounted, as for example you can use get a card for 3300 yen worth of travel, and pay 3000 yen, but it only covers subways and buses.

The Surutto Kansai Card covers subways and buses, plus Keihan, Hankyu, and other rail lines (BUT NOT JR).

Am I allowed to top up with 100 cash upon getting off the bus?

In case of subways, you can use remaining money on card instead of cash at vending machines.

In case of buses, I am not sure if it is possible to use remaining money on the card to partially pay for the ticket, but I suspect that it is possible. If I were you, I would try. And in case that it fails, keep 220 Yen in coins ready as an alternative.

By the way, note that the general name of the prepaid card is just "Surutto Kansai Card". The "Miyako Card" part is the company-specific alternative name of the card if you buy it through Kyoto City Bus or the subway. If you buy the card through different transportation companies, such as Keihan or Hankyu Railways, the card will be known under different alternative names such as K Card or Lagare Card. But these are all "Surutto Kansai Cards". I mention this because I was confused about it in the beginning.

Secondly, the Traffica Kyoto Card is of better value as there is a discount (unlike the Surutto), but it is not as extensive as the Surutto Kansai Miyako Card, right?

Yes, that is right. The Traffica Kyoto Card is only valid on Kyoto City Buses and Kyoto subways, while the Surutto Kansai Card can be used on virtually all buses, subways and trains in and around Kyoto, Osaka, Nara and Kobe with the exception of JR trains.

So if in Kyoto I only intend to visit Arashimaya and the Philosopher's Walk as some attractions surrounding those areas(while holding the JR Pass) it is better for me to purchase the Traffica? Unless I visit the Roanji or Kinkakuji Temples using the Keifuku line from Arashimaya.

Access to Arashiyama is recommended by train (JR, Keifuku or Hankyu) because buses can get stuck in traffic and can be very slow. Therefore, the Traffica Card will not be very useful.

Personally, I would not bother about the 10% discount given by the Traffica Card and rather go for the Surutto Kansai Card.

Yeah, you are right... At least I won't be saddled with a limited choice of transportation. Another thing, with travel around Roanji, would the flat rate still apply to those area?

Yes, Ryoanji is still inside the central Kyoto area, where the flat rate of 220 Yen applies to bus rides on Kyoto City Buses.

Does the Surutto Kansia Miyako Card cover ALL areas for the Kintetsu railway?

For example, I will already have a J-Rail pass but if I want to see the Ninja museum near Uenoshi station will the card's credit be valid for this region (still on the Kintetsu system)?

Will its credit also be valid if I want to take a limited express train (say KYOTO to KINTETSUNARA)?

The site only has the 3-day pass available in English so I can't get any information on how far the boundaries work for the Kansai Miyako Card.

Also, I would assume that even though it is a Kansai card, it does not include the same special promotions at tourism facilities as the Kansai Thru pass, right?

Thanks in advance!

On the Limited Express train part from Kyoto to Nara. It will cover the base fare, but if you want to ride a Limited Express train you would have to pay an extra supplement to ride the Limited Express train. Otherwise Kintetsu runs express trains that don't require an extra supplement.

If you already have a Japan Rail Pass, i would just ride JR from Kyoto to Nara.

All your transportation options to Nara:
http://www.japan-guide.com/e/e4107.html

Does the Surutto Kansia Miyako Card cover ALL areas for the Kintetsu railway?

No, basically it does not cover the area east of Nara Prefecture.

For example, I will already have a J-Rail pass but if I want to see the Ninja museum near Uenoshi station will the card's credit be valid for this region (still on the Kintetsu system)?

Only as far as Iga Kanbe Station. The remaining portion (Kintetsu Iga Line) is not covered.

Will its credit also be valid if I want to take a limited express train (say KYOTO to KINTETSUNARA)?

As explained by John, you would have to purchase the limited express fee separately.

Also, I would assume that even though it is a Kansai card, it does not include the same special promotions at tourism facilities as the Kansai Thru pass, right?

That's right.